Variant report

Variant	rs7313074
Chromosome Location	chr12:57154489-57154490
allele	A/G
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	CEBPB	chr12:57154407-57154582	HepG2	liver:	n/a	chr12:57154461-57154472
2	CEBPB	chr12:57154381-57154512	HepG2	liver:	n/a	chr12:57154461-57154472

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57081014..57083953-chr12:57153407..57154995,2	MCF-7	breast:
2	chr12:57151760..57156015-chr12:57398737..57401426,4	MCF-7	breast:

Variant related genes	Relation type
HSD17B6	TF binding region
ENSG00000110958	Chromatin interaction
ENSG00000166860	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1026565	0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10459246	0.89[ASN][1000 genomes]
rs10459247	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs10747770	0.96[ASN][1000 genomes]
rs10783796	0.90[ASN][1000 genomes]
rs10876916	0.93[CHB][hapmap]
rs10876918	0.94[ASN][1000 genomes]
rs1107479	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs11171914	0.92[CHB][hapmap]
rs11171917	0.81[AMR][1000 genomes]
rs11171951	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11171956	0.88[ASN][1000 genomes]
rs11171986	0.85[JPT][hapmap];0.88[MEX][hapmap]
rs1131514	0.94[ASN][1000 genomes]
rs11837319	0.83[AMR][1000 genomes]
rs12227117	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12229457	0.93[CHB][hapmap]
rs12828563	0.89[ASN][1000 genomes]
rs1465081	0.81[AMR][1000 genomes]
rs1466382	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1563896	0.87[CHB][hapmap]
rs1975875	0.94[ASN][1000 genomes]
rs1979325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2035081	0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2035082	0.90[ASN][1000 genomes]
rs2255074	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2290893	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2290894	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2926741	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2926743	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2926747	0.86[ASN][1000 genomes]
rs2926748	0.90[ASN][1000 genomes]
rs2950387	0.80[CHB][hapmap]
rs2950390	0.93[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs2958123	0.93[CHB][hapmap]
rs2958127	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2958130	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2958132	0.94[ASN][1000 genomes]
rs2958134	0.87[ASN][1000 genomes]
rs2958139	0.87[TSI][hapmap]
rs2958145	0.83[AMR][1000 genomes]
rs2958148	0.88[ASN][1000 genomes]
rs2958149	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2958153	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes]
rs2958154	0.93[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs2958155	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs3214051	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4277148	0.85[JPT][hapmap]
rs4759254	0.81[CHB][hapmap]
rs4759256	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902	0.90[ASN][1000 genomes]
rs7137749	0.83[ASN][1000 genomes]
rs7295862	0.88[ASN][1000 genomes]
rs7966391	0.91[ASN][1000 genomes]
rs7967600	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7978685	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7980317	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs898609	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs898611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs941207	0.86[CHB][hapmap]
rs9634246	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1794914	chr12:57119236-57195379	Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv826382	chr12:57151464-57208607	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7313074	RBMS2	cis	multi-tissue	Pritchard
rs7313074	KRT1	cis	cerebellum	SCAN
rs7313074	PRIM1	cis	parietal	SCAN
rs7313074	GPR182	cis	parietal	SCAN
rs7313074	HSD17B6	cis	cerebellum	SCAN
rs7313074	CELA1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57146400-57160400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57152200-57161800	Weak transcription	Pancreas	Pancrea
3	chr12:57153600-57155000	Enhancers	HepG2	liver
4	chr12:57153800-57155000	Flanking Active TSS	Liver	Liver
5	chr12:57153800-57155800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:57153800-57158000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:57154400-57154600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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