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Canine variant index

Variants in the Sniff Atlas

The Sniff Atlas v1.0.1 carries 9,667,790 common canine variants across 188 breeds on CanFam4 (UU_Cfam_GSD_1.0). This index lists the 15 trait loci with rich, hand-curated pages: body size, leg length, coat, ear set, brachycephaly. The remaining 9.67 million variants are queryable directly against the Zenodo sites VCF and through the Sniff MCP at mcp.sniff.world.

Query any of the 9.67 million

For any CanFam4 position, run bcftools/tabix directly against the Atlas sites VCF (download from the Zenodo record): 

tabix sniff_atlas.sites.vcf.gz 5:56189113

Returns global AF, popmax breed, ESM2 LLR, Pangolin score, phyloP 241-way, SnpEff consequence in the INFO column. The Sniff MCP server is live at mcp.sniff.world (Streamable HTTP) with REST mirror at api.sniff.world/v1/; agent-callable variant lookups from Claude, ChatGPT, Cursor, or any conformant client work today.

Trait-loci tier (15 variants)
body size
chr3:41,004,018 (G/A)

ADAMTS17

height/eye locus chr3

body size
chr10:8,752,420 (C/T)

HMGA2

small breeds enriched at chr10:8-12Mb

body size
chr15:41,555,463 (C/A)

IGF1

small breeds enriched for short-allele haplotype

body size
chr3:91,717,919 (A/G)

LCORL

NCAPG/LCORL height locus chr3

body size
chr7:43,693,994 (A/G)

SMAD2

small vs giant strong differentiation chr7

body size
chr4:40,056,722 (C/A)

STC2

size locus chr4

brachycephaly
chr32:34,757,273 (C/T)

BMP3

short-face candidate

brachycephaly
chr1:56,398,416 (A/G)

SMOC2

short-face candidate

coat color
chr5:63,544,121 (T/C)

MC1R

recessive red e/e; Ensembl symbol fails; chr5 region

coat curl
chr27:44,171,053 (T/C)

KRT71

curly-coat variant; backbone coverage poor

coat furnishings
chr13:8,844,479 (C/T)

RSPO2

wirehaired/furnished breeds

coat length
chr32:35,481,592 (T/C)

FGF5

long-hair allele

ear type
chr10:8,230,753 (G/A)

MSRB3

erect vs drop; size-confounded with HMGA2 chr10

leg length
chr12:34,964,869 (T/C)

FGF4_retrogene_CFA12

chondrodystrophy insertion site; not annotated as gene

leg length
chr18:20,697,946 (T/C)

FGF4_retrogene_CFA18

chondrodysplasia insertion site; not annotated as gene