Variant report

Variant	rs12629483
Chromosome Location	chr3:75097188-75097189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11709921	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11920209	0.90[ASN][1000 genomes]
rs12054293	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054432	0.94[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12171270	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486094	0.91[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12488229	0.81[ASW][hapmap];0.94[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs12494321	0.87[ASN][1000 genomes]
rs12496883	0.87[ASN][1000 genomes]
rs12632116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632660	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636203	0.83[ASN][1000 genomes]
rs12636209	0.83[ASN][1000 genomes]
rs4073454	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4076158	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4076688	0.91[ASN][1000 genomes]
rs4298078	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340743	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4346587	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4349537	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356853	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4368539	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449358	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4467494	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4544657	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4589972	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607148	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4635750	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677447	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4677449	0.90[ASN][1000 genomes]
rs4677458	0.88[ASN][1000 genomes]
rs4677473	0.83[ASN][1000 genomes]
rs5009222	0.94[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs62258901	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62266825	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62267777	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6549681	0.91[ASN][1000 genomes]
rs6549685	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6549689	0.91[ASN][1000 genomes]
rs6761963	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6786444	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6796018	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801622	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72628656	0.81[ASN][1000 genomes]
rs7430106	0.88[ASN][1000 genomes]
rs7616253	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652902	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9310311	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815881	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9816018	0.91[ASN][1000 genomes]
rs9825398	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9829306	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9833132	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835668	0.91[ASN][1000 genomes]
rs9842069	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9845814	0.88[ASN][1000 genomes]
rs9850353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863946	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9865292	0.88[ASN][1000 genomes]
rs9868696	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869833	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9869924	0.87[ASN][1000 genomes]
rs9877977	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9881282	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9882460	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529994	chr3:74720752-75471887	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv916594	chr3:74943399-75540161	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv1851336	chr3:74970564-75280989	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1005139	chr3:75027834-75168557	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv534344	chr3:75028665-75164716	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv834736	chr3:75083055-75271458	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12629483	FAM86DP	cis	parietal	SCAN
rs12629483	BIN1	trans	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:75092600-75097200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:75094800-75097200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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