Variant report

Variant	rs12632346
Chromosome Location	chr3:161020975-161020976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:161008825..161011229-chr3:161019509..161021871,2	MCF-7	breast:
2	chr3:161020177..161024858-chr3:161085049..161092836,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12108169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374001	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12629152	1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12629929	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12630038	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12631467	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12633103	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12636434	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12636573	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12636590	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1478568	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs16834031	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1904204	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28853731	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4132373	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4443189	1.00[CEU][hapmap]
rs55949838	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56174161	0.84[AMR][1000 genomes]
rs56741879	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56890199	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57441646	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59827519	0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs60228180	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60277631	0.89[AMR][1000 genomes]
rs60801542	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61193379	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61578814	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61596736	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6770585	1.00[CEU][hapmap]
rs73875456	0.84[AMR][1000 genomes]
rs73875458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73875460	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73875464	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73875472	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73875473	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73875482	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73875492	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73875500	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73875502	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73878303	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73878304	0.80[ASN][1000 genomes]
rs7613358	0.90[JPT][hapmap]
rs9871480	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	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
4	nsv4091	chr3:161018540-161063875	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12632346	C3orf57	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161017000-161021400	Weak transcription	Aorta	Aorta
2	chr3:161017000-161033000	Weak transcription	Left Ventricle	heart
3	chr3:161017600-161032600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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