gnomancer · raw DNA report

demo_AncestryDNA.txt · generated 2026-11-06 15:51 · gnomancer v0.5.1

Computed locally from a consumer genotyping array. The array reports a fixed list of common sites, not your whole genome; absence of a variant here never means a gene is normal, and single-marker readings are probabilistic. This is not medical advice. Discuss anything concerning with a clinician or genetic counselor and confirm with a clinical-grade test before acting on it.

At a glance

Who the data says you are

Blood group O (Rh not typed).
Lactose: non-persistent.
Bitter taste: PAV/AVI or mixed: medium taster.

Worth knowing

G6PD A- (V68M): carrier / affected if male.
NOD2 G908R (Crohn's): carrier.
LPA High Lp(a) tag: elevated Lp(a) likely (~2x CAD odds); a direct Lp(a) blood test is cheap.
GBA N370S (Gaucher / Parkinson's): carrier: ~5x Parkinson's odds; Gaucher carrier.
One copy of a risk allele at: HLA-DQB1 (DQ8 tag (celiac)), TCF7L2 (Type 2 diabetes), CDKN2B-AS1 (9p21) (Coronary artery disease). Population-average territory, listed for completeness.
CYP2C9 *2 (R144C): one *2: reduced warfarin/NSAID/phenytoin metabolism.
CYP2C9 *3 (I359L): one *3: markedly reduced metabolism.
VKORC1 1173C>T (proxy for -1639): sensitive.
ABCG2 Q141K: homozygous reduced.
HCP5 HLA-B*57:01 tag: HLA-B*57:01 carrier: abacavir hypersensitivity, avoid.

Reassuring

CLU: two protective alleles.
APOE e3/e3: most common genotype, reference risk for Alzheimer's and lipids.
Negative at 28 checked health and carrier sites, including F5, F2, HFE, MTHFR, HLA-DQA1, HLA-DRB1, PTPN22, CFH.
No runs of homozygosity ≥3 Mb.
The file itself passed every quality check.

Sensible next steps

Keep the pharmacogenomic table handy for any prescriber (the one-page card next to this report, pgx-card.pdf, is made for that); a clinical PGx panel confirms it and covers the sites the chip misses.

Overview

Vendor

AncestryDNA

build GRCh37

Sites

20,342

0.00% no-call

Genetic sex

Female

from X heterozygosity and Y calls

Y haplogroup

—

skipped (sample is not male)

mtDNA haplogroup

—

skipped (--no-mt)

Blood group

Rh not typed

✓Quality checks passed. Call rate, heterozygosity and sex markers are all in the expected range.

Lineages

Two tiny slices of the genome are inherited along a single line: the Y chromosome from father to son, and mitochondrial DNA from mother to child. Each carries a lineage label (haplogroup) with a known geographic history. They describe one ancestral line each, not your overall ancestry.

Paternal line · Y chromosome

Not called: skipped (sample is not male)

Maternal line · mitochondrial DNA

Not called: skipped (--no-mt)

Combined readings

Results that depend on more than one site read together: blood group, lactase persistence, bitter taste and APOE.

ABO blood group

Rh factor is not typed on consumer arrays; A1 vs A2 subgroups not distinguished

rs8176719 DD, rs8176746 TG

Lactase persistence

non-persistent (likely adult lactose intolerance)

Based on the European -13910 and -22018 variants; African and Middle Eastern persistence alleles (rs41380347, rs145946881, rs41525747) are usually not on consumer arrays

TAS2R38 bitter taste (PTC/PROP)

PAV/AVI or mixed: medium taster

haplotype score 5/6 across the three defining SNPs

APOE (Alzheimer's risk genotype)Collapsed on purpose. Some people prefer not to learn this result; open it only if you want to.

APOE

e3/e3

most common genotype, reference risk for Alzheimer's and lipids · rs429358 TT, rs7412 CC

Marker panel

Each row is one well-studied site. The badge counts how many copies of the effect allele you carry (0, 1 or 2) on the GRCh37 forward strand. The share column says what fraction of the European reference population (1000 Genomes) is expected to carry the same genotype; hover it for all five world regions. "Not on array" means this vendor's chip does not type the site.

Ancestry-informative markers

Sites whose allele frequencies differ strongly between world regions. Together with the Y and mtDNA lineages they hint at ancestry; they are not an admixture estimate.

Swipe sideways for genotype, effect allele and reading.

Marker	Gene	What it tags	Genotype	Effect allele	How common (EUR)	Reading
rs1426654	SLC24A5 rs1426654	Skin pigmentation A111T	AG	1/2 A	1%	one light-skin allele
rs16891982	SLC45A2 rs16891982	Skin/hair pigmentation L374F	GC	1/2 G	12%	one European light-pigmentation allele
rs3827760	EDAR rs3827760	V370A hair thickness / shovel incisors	GA	1/2 G	2%	one copy of the East Asian/Native American allele
rs2814778	ACKR1 (DARC) rs2814778	Duffy null (FY*O)	CT	1/2 C	1%	one Duffy-null allele (common in West/Central African ancestry)
rs4988235	LCT rs4988235	Lactase persistence -13910	GG	0/2 A	24%	non-persistent at this site the European persistence allele; other populations use different alleles
rs182549	LCT rs182549	Lactase persistence -22018	CC	0/2 T	24%	non-persistent at this site
rs671	ALDH2 rs671	ALDH2*2 alcohol flush	GA	1/2 A	0%	flush reaction, reduced acetaldehyde clearance (common in East Asia)
rs1229984	ADH1B rs1229984	ADH1B*2 (His48)	CC	0/2 T	94%	1/1 typical of Europe and Africa

Traits

Common variants with well-replicated effects on visible or sensory traits. Most are probabilistic, not deterministic.

Swipe sideways for genotype, effect allele and reading.

Marker	Gene	What it tags	Genotype	Effect allele	How common (EUR)	Reading
rs12913832	HERC2 rs12913832	Eye color (main determinant)	GA	1/2 G	46%	brown or hazel likely, green possible
rs1800407	OCA2 rs1800407	Eye color modifier R419Q	TC	1/2 T	14%	green/hazel modifier present
rs12896399	SLC24A4 rs12896399	Eye/hair color	GG	0/2 T	32%	darker-associated
rs1042602	TYR rs1042602	S192Y pigmentation / freckling	CC	0/2 A	39%	no lighter allele
rs1393350	TYR rs1393350	Eye/hair color	AG	1/2 A	37%	intermediate
rs12203592	IRF4 rs12203592	Freckles, lighter hair, sun sensitivity	TT	2/2 T	1%	freckles and sun sensitivity likely
rs1805007	MC1R rs1805007	R151C red hair	CT	1/2 T	13%	red-hair carrier (R allele)
rs1805008	MC1R rs1805008	R160W red hair	CT	1/2 T	12%	red-hair carrier (R allele)
rs1805009	MC1R rs1805009	D294H red hair	GG	0/2 C	98%	no variant
rs1805006	MC1R rs1805006	D84E red hair	CC	0/2 A	98%	no variant
rs11547464	MC1R rs11547464	R142H red hair	GG	0/2 A	98%	no variant
rs1110400	MC1R rs1110400	I155T red hair	TT	0/2 C	98%	no variant
rs885479	MC1R rs885479	R163Q (weak variant)	GA	1/2 A	13%	one weak r allele
rs11803731	TCHH rs11803731	Hair curl (European)	TT	0/2 A	5%	curlier-associated
rs17822931	ABCC11 rs17822931	Earwax type / underarm odor	CC	0/2 T	75%	wet earwax, typical body odor
rs4481887	OR2M7 region rs4481887	Asparagus metabolite smell	GG	0/2 A	52%	less likely to smell it
rs10427255	ZEB2 region rs10427255	Photic sneeze reflex	TC	1/2 C	50%	intermediate
rs1815739	ACTN3 rs1815739	R577X sprint/power muscle	CC	0/2 T	32%	RR: two working copies, power-leaning
rs762551	CYP1A2 rs762551	Caffeine metabolism *1F	CA	1/2 C	44%	intermediate
rs2472297	CYP1A1/2 region rs2472297	Caffeine intake tendency	CC	0/2 T	62%	lower-intake alleles
rs4410790	AHR rs4410790	Caffeine intake tendency	TT	0/2 C	15%	lower-intake alleles
rs713598	TAS2R38 rs713598	Bitter taste PTC (A49P)	GG	2/2 G	—	taster see combined TAS2R38 reading
rs1726866	TAS2R38 rs1726866	Bitter taste (V262A)	GA	1/2 G	—	taster see combined TAS2R38 reading
rs10246939	TAS2R38 rs10246939	Bitter taste (I296V)	CC	2/2 C	—	taster see combined TAS2R38 reading
rs72921001	OR6A2 rs72921001	Cilantro soapy taste	AC	1/2 C	46%	one soapy-taste allele
rs9939609	FTO rs9939609	BMI/obesity risk	TT	0/2 A	34%	no risk allele
rs17782313	MC4R rs17782313	BMI	TT	0/2 C	58%	no risk allele
rs16969968	CHRNA5 rs16969968	Nicotine dependence D398N	GG	0/2 A	40%	no risk allele
rs4680	COMT rs4680	Val158Met	GA	1/2 A	50%	Val/Met popular but weak-effect marker
rs6265	BDNF rs6265	Val66Met	CT	1/2 T	32%	Val/Met weak-effect marker
rs1799971	OPRM1 rs1799971	A118G	GA	1/2 G	27%	one G allele weak-effect marker
rs601338	FUT2 rs601338	Secretor status W154X	GG	0/2 A	31%	secretor
rs2180439	PAX1 region rs2180439	Male pattern hair loss	TC	1/2 C	49%	one risk allele
rs53576	OXTR rs53576	Oxytocin receptor	GG	0/2 A	42%	no variant allele weak-effect marker, popular online but poorly replicated
rs1800497	ANKK1/DRD2 rs1800497	TaqIA	GG	0/2 A	66%	A2/A2 weak-effect marker
rs8176719	ABO rs8176719	O allele (261delG)	DD	2/2 D	37%	blood group O see combined ABO reading
rs8176746	ABO rs8176746	B allele	TG	1/2 T	—	one B allele see combined ABO reading

Health-associated common variantsCollapsed on purpose: contains disease-risk and carrier results. Open when you are ready, or use "Reveal health sections" above.

Health-associated common variants

Common variants that shift the odds of a condition. Odds ratios are from population studies; absolute risk depends on far more than one site.

Swipe sideways for genotype, effect allele and reading.

Marker	Gene	What it tags	Genotype	Effect allele	How common (EUR)	Reading
rs1050828	G6PD rs1050828	G6PD A- (V68M)	TC	1/2 T	—	carrier / affected if male X-linked; hemizygous in males
rs429358	APOE rs429358	e4-defining site (C112R)	TT	0/2 C	71%	no e4 allele see combined APOE reading
rs7412	APOE rs7412	e2-defining site (R158C)	CC	0/2 T	88%	no e2 allele see combined APOE reading
rs6025	F5 rs6025	Factor V Leiden R506Q	CC	0/2 T	98%	negative
rs1799963	F2 rs1799963	Prothrombin G20210A	GG	0/2 A	98%	negative
rs1800562	HFE rs1800562	Hemochromatosis C282Y	GG	0/2 A	92%	negative
rs1799945	HFE rs1799945	Hemochromatosis H63D	CC	0/2 G	69%	negative
rs1800730	HFE rs1800730	S65C	AA	0/2 T	97%	negative
rs1801133	MTHFR rs1801133	C677T (A222V)	GG	0/2 A	40%	normal activity widely over-interpreted online
rs1801131	MTHFR rs1801131	A1298C	TT	0/2 G	47%	normal
rs2187668	HLA-DQA1 rs2187668	DQ2.5 tag (celiac)	CC	0/2 T	80%	no DQ2.5
rs7454108	HLA-DQB1 rs7454108	DQ8 tag (celiac)	TC	1/2 C	—	DQ8 present
rs3135388	HLA-DRB1 rs3135388	DRB1*15:01 tag (multiple sclerosis)	GG	0/2 A	77%	non-carrier
rs2476601	PTPN22 rs2476601	R620W autoimmunity	GG	0/2 A	82%	negative
rs2066844	NOD2 rs2066844	R702W (Crohn's)	CC	0/2 T	90%	negative
rs2066845	NOD2 rs2066845	G908R (Crohn's)	GC	1/2 C	2%	carrier
rs7903146	TCF7L2 rs7903146	Type 2 diabetes	CT	1/2 T	43%	one risk allele (~1.4x odds) strongest common T2D variant
rs1061170	CFH rs1061170	Y402H macular degeneration	TT	0/2 C	41%	no risk allele smoking interacts strongly
rs10490924	ARMS2 rs10490924	A69S macular degeneration	GG	0/2 T	65%	no risk allele
rs1333049	CDKN2B-AS1 (9p21) rs1333049	Coronary artery disease	GC	1/2 C	50%	one copy (~1.25x)
rs10455872	LPA rs10455872	High Lp(a) tag	AG	1/2 G	14%	elevated Lp(a) likely (~2x CAD odds); a direct Lp(a) blood test is cheap
rs3798220	LPA rs3798220	I4399M high Lp(a)	TT	0/2 C	98%	no high-Lp(a) allele
rs11136000	CLU rs11136000	Alzheimer's (protective T)	TT	2/2 T	15%	two protective alleles
rs75932628	TREM2 rs75932628	R47H Alzheimer's	CC	0/2 T	99%	negative
rs76763715	GBA rs76763715	N370S (Gaucher / Parkinson's)	TC	1/2 C	—	carrier: ~5x Parkinson's odds; Gaucher carrier
rs34637584	LRRK2 rs34637584	G2019S Parkinson's	GG	0/2 A	100%	negative
rs2802292	FOXO3 rs2802292	Longevity-associated	TT	0/2 G	32%	no longevity allele
rs1800629	TNF rs1800629	-308 promoter	GG	0/2 A	75%	no variant allele weak-effect marker

Carrier and rare pathogenic sitesCollapsed on purpose: contains disease-risk and carrier results. Open when you are ready, or use "Reveal health sections" above.

Carrier and rare pathogenic sites

A handful of well-known pathogenic variants that happen to be on consumer chips. A negative here covers only this one site, not the gene.

Swipe sideways for genotype, effect allele and reading.

Marker	Gene	What it tags	Genotype	Effect allele	How common (EUR)	Reading
rs113993960	CFTR rs113993960	deltaF508 cystic fibrosis	II	0/2 D	—	negative arrays type 1-3 CFTR sites of 2000+
rs333	CCR5 rs333	delta32	II	0/2 D	—	negative
rs80357906	BRCA1 rs80357906	185delAG (Ashkenazi founder)	II	0/2 D	—	negative at this site
rs80359550	BRCA2 rs80359550	6174delT (Ashkenazi founder)	II	0/2 D	—	negative at this site
rs11571833	BRCA2 rs11571833	K3326X	AA	0/2 T	98%	negative
rs334	HBB rs334	Sickle cell HbS	TT	0/2 A	100%	negative
rs33930165	HBB rs33930165	HbC	CC	0/2 T	100%	negative
rs33950507	HBB rs33950507	HbE	CC	0/2 T	100%	negative

Pharmacogenomic sites (single markers)

Variants that change how drugs are metabolized. Useful to mention to a prescriber; clinical decisions need a clinical-grade test.

Swipe sideways for genotype, effect allele and reading.

Marker	Gene	What it tags	Genotype	Effect allele	How common (EUR)	Reading
rs1799853	CYP2C9 rs1799853	*2 (R144C)	TC	1/2 T	22%	one *2: reduced warfarin/NSAID/phenytoin metabolism
rs1057910	CYP2C9 rs1057910	*3 (I359L)	CA	1/2 C	13%	one *3: markedly reduced metabolism
rs28371686	CYP2C9 rs28371686	*5	GG	2/2 G	0%	5/5
rs9332131	CYP2C9 rs9332131	*6	II	0/2 D	—	no *6
rs28371685	CYP2C9 rs28371685	*11	CC	0/2 T	100%	no *11
rs4244285	CYP2C19 rs4244285	*2 (loss of function)	GA	1/2 A	25%	one *2: intermediate metabolizer (clopidogrel less effective)
rs4986893	CYP2C19 rs4986893	*3 (loss of function)	GA	1/2 A	0%	one *3 mostly East Asian
rs12248560	CYP2C19 rs12248560	*17 (increased function)	TC	1/2 T	35%	one *17: rapid metabolizer
rs9923231	VKORC1 rs9923231	-1639G>A warfarin sensitivity	CC	0/2 T	37%	normal warfarin dose requirement
rs9934438	VKORC1 rs9934438	1173C>T (proxy for -1639)	AA	2/2 A	15%	sensitive in near-perfect LD with rs9923231
rs2108622	CYP4F2 rs2108622	V433M	CT	1/2 T	41%	slightly higher warfarin dose
rs3892097	CYP2D6 rs3892097	*4 (null)	CC	0/2 T	—	no *4 CNV not detectable on arrays
rs1065852	CYP2D6 rs1065852	10 (reduced) / also on 4	GG	0/2 A	—	no *10
rs28371725	CYP2D6 rs28371725	*41 (reduced)	CT	1/2 T	—	one *41
rs776746	CYP3A5 rs776746	3 vs 1 (expressor)	TC	1/2 T	11%	1/3 expressor: higher tacrolimus dose
rs3745274	CYP2B6 rs3745274	*6 (516G>T)	GG	0/2 T	58%	1/1
rs4149056	SLCO1B1 rs4149056	*5 (V174A) statin myopathy	TC	1/2 C	27%	one C: ~4x simvastatin myopathy risk
rs2231142	ABCG2 rs2231142	Q141K	TT	2/2 T	1%	homozygous reduced
rs3918290	DPYD rs3918290	*2A (IVS14+1G>A)	CC	0/2 T	99%	normal
rs67376798	DPYD rs67376798	D949V	TT	0/2 A	99%	normal
rs887829	UGT1A1 rs887829	*28 proxy (Gilbert)	CT	1/2 T	42%	one *28
rs4148323	UGT1A1 rs4148323	*6 (G71R)	GA	1/2 A	1%	one *6 mostly East Asian
rs1801280	NAT2 rs1801280	*5 (I114T)	TT	0/2 C	30%	no 5 combine with 6/*7
rs1799930	NAT2 rs1799930	*6 (R197Q)	GA	1/2 A	41%	one slow allele
rs1799931	NAT2 rs1799931	*7 (G286E)	GA	1/2 A	4%	one slow allele
rs1495741	NAT2 rs1495741	acetylator tag	AG	1/2 G	37%	intermediate
rs1800460	TPMT rs1800460	*3B	CT	1/2 T	5%	one *3B (thiopurine dose reduction)
rs1142345	TPMT rs1142345	*3C	CC	2/2 C	0%	3C/3C
rs2395029	HCP5 rs2395029	HLA-B*57:01 tag	GT	1/2 G	8%	HLA-B*57:01 carrier: abacavir hypersensitivity, avoid
rs1800566	NQO1 rs1800566	P187S (*2)	GA	1/2 A	33%	one null allele

ClinVar scan of every typed site

The curated panel above covers about a hundred sites. This pass checks every site on the chip against ClinVar, the public archive of clinically classified variants, and lists any pathogenic or likely-pathogenic allele you carry. Each hit is scored for plausibility, because arrays are unreliable at rare sites.

ClinVar findingsCollapsed on purpose: may contain carrier states and disease-risk variants. Open when ready.

skipped (--no-clinvar)

Drug-gene results (PharmCAT)

PharmCAT (PharmGKB) assigns star-allele diplotypes and CPIC phenotypes per gene from the sites the chip typed. It is the CPIC-aligned caller used in clinical research pipelines, but here it sees only a fraction of each gene's defining positions.

skipped (--no-pharmcat)

Quality

How complete and internally consistent the file is. These numbers say nothing about you; they say whether the rest of the report can be trusted.

No-calls: 0 of 20,342 (0.00%)
Indel probes: 6 (insertion/deletion sites, reported as I/D)
Autosomal heterozygosity: 0.326
X heterozygosity: 0.2483
Y sites called: 0 / 0
Genetic sex: Female (file header: Female)

Share of called sites that are heterozygous, per chromosome. Autosomes typically sit between 0.25 and 0.35 on consumer arrays. X near zero with Y present indicates a male sample; MT is always homozygous.

Runs of homozygosity

Long stretches where both copies of a chromosome are identical. They appear when parents share recent ancestors, and in populations with founder effects.

No runs of homozygosity ≥3 Mb: no sign of recent parental relatedness.

How this was computed

Every step runs on this computer from the raw file. Tool versions and references, for reproducibility.

Step	Tool	Reference
Parsing and build detection	snps 2.12.1	github.com/apriha/snps; remapped to GRCh37 when needed
Marker panel and frequencies	gnomancer 0.5.1	111 curated sites; Hardy-Weinberg from 1000 Genomes phase 3 allele frequencies (Ensembl GRCh37)
Report	gnomancer 0.5.1	generated from AncestryDNA data, build GRCh37

Glossary

Terms used in this reportOpen for one-line definitions.

Haplogroup: A branch of the human family tree defined by shared mutations on the Y chromosome (paternal line) or mitochondrial DNA (maternal line). It describes one ancestral line, not overall ancestry.
Site / marker / SNP: One position in the genome where people differ. A consumer chip types a fixed list of around 600,000 of them; this report calls them sites.
rsID: The public catalogue number for a site, e.g. rs4988235. Useful for looking a site up in SNPedia or ClinVar.
Genotype: The two letters you carry at a site, one from each parent (one letter on X or Y in males).
Effect allele: The version of a site that the published association is about. The badge counts how many copies you carry: 0, 1 or 2.
Heterozygous / homozygous / hemizygous: Two different letters at a site / two of the same / only one copy present (X and Y in males, and mitochondrial DNA).
Carrier: One copy of a variant for a recessive condition. Carriers are usually unaffected; the result matters mainly for children, if the other parent carries one too.
Odds ratio (e.g. ~2x): How much a variant multiplies the odds of a condition in population studies. It is relative, not absolute: 2x of a 1% risk is 2%.
Run of homozygosity: A long stretch where both chromosome copies match, which happens when parents share recent ancestors.
Diplotype / star allele: A pharmacogenomics term for the pair of gene versions you carry, named *1, *2, *3 and so on; the pair determines a metabolizer phenotype.
Phenotype (metabolizer): What the diplotype predicts: normal, intermediate, poor or rapid metabolism of certain drugs.
ClinVar: The public NIH archive of variants and their clinical classifications, with a review status from zero to four stars.
GRCh37 / build 37: The version of the human reference genome that consumer vendors report positions against; files on build 38 are remapped.
1000 Genomes: A public reference set of about 2,500 genomes from 26 populations; the source of the "how common" percentages.

What this file cannot tell you

Rare pathogenic variants. The chip targets common variation; genes like BRCA1/2 and CFTR are covered at a handful of sites only.
Copy-number genes such as CYP2D6, and full HLA types beyond tag SNPs.
Admixture percentages at the resolution of the vendor's own report, which uses a proprietary reference panel.
Anything at sites the vendor did not type. PharmCAT assumes the reference allele at untyped positions, so a "complete" diplotype can still miss a rare allele.
For a male sample, X-chromosome sites have one copy (hemizygous), so "carrier" and "homozygous" do not apply there in the usual sense.
"How common" uses the European reference population unless --ancestry placed you in another 1000 Genomes group; a different reference changes those percentages, not your genotype.