Variant report

Variant	rs12632686
Chromosome Location	chr3:161069078-161069079
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160992668..160995441-chr3:161067329..161069400,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12631095	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12631808	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12632351	1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12632514	1.00[EUR][1000 genomes]
rs12632632	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634006	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12634319	1.00[JPT][hapmap]
rs12634781	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12635895	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12639236	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16832385	1.00[EUR][1000 genomes]
rs2404345	1.00[EUR][1000 genomes]
rs462514	0.88[JPT][hapmap]
rs55914832	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56230831	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56378191	1.00[EUR][1000 genomes]
rs57175632	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57212203	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58013864	1.00[EUR][1000 genomes]
rs58404146	1.00[EUR][1000 genomes]
rs58550445	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59761692	0.86[ASN][1000 genomes]
rs60172527	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61217744	0.86[ASN][1000 genomes]
rs61631170	1.00[EUR][1000 genomes]
rs72494862	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72494864	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73021435	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73875481	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73875497	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73875623	1.00[EUR][1000 genomes]
rs73878306	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73878307	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs73878308	0.86[ASN][1000 genomes]
rs73878311	0.86[ASN][1000 genomes]
rs73878333	1.00[EUR][1000 genomes]
rs73878336	1.00[EUR][1000 genomes]
rs873183	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs896080	1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
4	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12632686	C3orf57	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161058200-161072200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:161060600-161070200	Weak transcription	Esophagus	oesophagus
4	chr3:161064400-161083000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:161065400-161069200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:161065800-161069200	Enhancers	NHEK	skin
7	chr3:161065800-161069600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:161066200-161069400	Enhancers	Hela-S3	cervix
9	chr3:161066600-161069200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:161067000-161069400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:161068200-161083200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:161068400-161075800	Weak transcription	Stomach Mucosa	stomach
13	chr3:161068400-161083200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:161068800-161069600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:161068800-161079000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:161069000-161070600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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