Variant report

Variant	rs12636434
Chromosome Location	chr3:161049534-161049535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:161049445-161049619	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160941286..160943781-chr3:161049353..161051751,2	MCF-7	breast:
2	chr3:160937993..160941056-chr3:161047965..161051023,3	MCF-7	breast:

Variant related genes	Relation type
PSMC1P7	TF binding region
ENSG00000169251	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11539155	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12108169	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12374001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12629152	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12629929	0.89[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12630038	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12631467	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12632346	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12633103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636573	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12636590	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1450530	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1478568	0.90[JPT][hapmap]
rs16832237	0.85[EUR][1000 genomes]
rs16834031	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1904204	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28384383	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28853731	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4132373	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55949838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174161	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56741879	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56890199	0.90[ASN][1000 genomes]
rs57441646	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59827519	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60228180	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs60277631	0.83[AMR][1000 genomes]
rs60801542	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61193379	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61388164	0.94[AMR][1000 genomes]
rs61578814	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61596736	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6800515	0.95[EUR][1000 genomes]
rs73162584	0.85[EUR][1000 genomes]
rs73162595	0.85[EUR][1000 genomes]
rs73162599	0.85[EUR][1000 genomes]
rs73875453	0.94[AMR][1000 genomes]
rs73875455	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73875456	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73875458	0.84[AMR][1000 genomes]
rs73875460	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73875464	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73875472	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73875473	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73875482	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73875492	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73875500	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73875502	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73878303	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73878304	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73878305	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7613358	0.91[JPT][hapmap]
rs7652447	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	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	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
4	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
5	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
rs12636434	C3orf57	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161048200-161051800	Enhancers	HepG2	liver

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