Variant report

Variant	rs10899116
Chromosome Location	chr11:75476195-75476196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75465856..75467458-chr11:75474012..75476887,2	K562	blood:
2	chr11:75475566..75477498-chr11:75506229..75507930,2	MCF-7	breast:
3	chr11:75474947..75476631-chr11:75479076..75481946,2	K562	blood:

Variant related genes	Relation type
ENSG00000062282	Chromatin interaction
ENSG00000247867	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10160802	1.00[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1017713	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10219339	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10793124	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10793125	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10793126	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10793127	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10793128	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10793129	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10793130	0.86[EUR][1000 genomes]
rs10793132	0.90[CEU][hapmap];0.93[CHB][hapmap];0.92[ASN][1000 genomes]
rs10793133	0.92[ASN][1000 genomes]
rs10793135	0.90[CEU][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs10899105	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10899109	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899110	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899112	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10899113	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899114	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10899115	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10899118	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs10899119	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899120	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899121	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.90[TSI][hapmap];0.94[ASN][1000 genomes]
rs10899122	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs10899123	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs10899124	0.90[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10899127	0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs10899128	0.90[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs10899129	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs10899131	0.92[ASN][1000 genomes]
rs10899132	0.92[ASN][1000 genomes]
rs10899133	0.92[ASN][1000 genomes]
rs10899134	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs10899135	0.92[ASN][1000 genomes]
rs10899136	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs10899137	0.92[ASN][1000 genomes]
rs10899138	0.89[CEU][hapmap];0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs10899139	0.88[ASN][1000 genomes]
rs10899140	0.88[ASN][1000 genomes]
rs10899141	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs10899142	0.88[ASN][1000 genomes]
rs10899144	0.86[ASN][1000 genomes]
rs10899145	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs11236507	0.83[ASN][1000 genomes]
rs11236508	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11236509	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11236511	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11236514	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11236515	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11236516	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11236517	0.90[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11236518	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11236519	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236525	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11236526	0.94[EUR][1000 genomes]
rs11236527	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236528	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11236531	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.90[TSI][hapmap];0.94[ASN][1000 genomes]
rs11236533	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11236534	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11236537	0.91[ASN][1000 genomes]
rs11236538	0.92[ASN][1000 genomes]
rs11236539	0.92[ASN][1000 genomes]
rs11236540	0.90[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs11236542	0.92[ASN][1000 genomes]
rs11236543	0.92[ASN][1000 genomes]
rs11236545	0.89[CEU][hapmap];0.86[CHB][hapmap];0.92[ASN][1000 genomes]
rs11236546	0.89[CEU][hapmap];0.93[CHB][hapmap];0.92[ASN][1000 genomes]
rs11236549	0.86[CEU][hapmap];0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs11236551	0.88[ASN][1000 genomes]
rs11236552	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs11236553	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs11236554	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs11236555	0.90[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11501918	0.94[ASN][1000 genomes]
rs11821808	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11822903	0.92[CHB][hapmap];0.93[ASN][1000 genomes]
rs11823869	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12222542	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs12222995	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12224062	0.88[ASN][1000 genomes]
rs12278224	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs12278257	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs12280456	0.81[CEU][hapmap]
rs12280464	0.81[CEU][hapmap];0.82[CHD][hapmap]
rs12285853	0.92[ASN][1000 genomes]
rs1458836	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs17134394	0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs1806895	0.94[EUR][1000 genomes]
rs2004638	1.00[CEU][hapmap]
rs2008476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2168947	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs28802056	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3060	0.90[CEU][hapmap]
rs36016715	0.82[ASN][1000 genomes]
rs3740849	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs3740850	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs531117	0.81[CHB][hapmap]
rs57188913	0.94[EUR][1000 genomes]
rs58340821	0.95[ASN][1000 genomes]
rs58411334	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59913369	0.94[EUR][1000 genomes]
rs60677263	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60692776	0.86[ASN][1000 genomes]
rs643884	0.81[CHB][hapmap]
rs644361	0.81[CHB][hapmap]
rs6592615	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs66784596	0.82[ASN][1000 genomes]
rs67233017	0.82[ASN][1000 genomes]
rs67268976	0.82[ASN][1000 genomes]
rs7101806	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs7106736	0.92[ASN][1000 genomes]
rs7107742	0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs7108178	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs7110517	0.92[ASN][1000 genomes]
rs7118039	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs7118293	0.94[ASN][1000 genomes]
rs7122123	0.88[ASN][1000 genomes]
rs7126727	0.90[CEU][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs7128716	0.92[ASN][1000 genomes]
rs72995678	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72997616	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72997623	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7933235	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs7944950	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7947418	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs7947512	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv897924	chr11:75424546-75678647	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv897925	chr11:75456134-75556323	Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10899116	DGAT2	cis	Whole Blood	GTEx
rs10899116	ARAP1	cis	parietal	SCAN
rs10899116	POLD3	cis	cerebellum	SCAN
rs10899116	RP11-535A19.1	cis	Whole Blood	GTEx
rs10899116	SLC43A2	trans	parietal	SCAN
rs10899116	B3GNT6	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75470200-75476200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr11:75472000-75476600	Enhancers	Adipose Nuclei	Adipose
3	chr11:75472400-75477000	Weak transcription	GM12878-XiMat	blood
4	chr11:75472600-75478600	Weak transcription	Fetal Intestine Small	intestine
5	chr11:75473400-75478400	Weak transcription	Lung	lung
6	chr11:75474600-75477400	Weak transcription	NHDF-Ad	bronchial
7	chr11:75474800-75479000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:75475200-75478200	Weak transcription	Spleen	Spleen
9	chr11:75475200-75479000	Weak transcription	Pancreas	Pancrea
10	chr11:75475400-75476200	Weak transcription	HepG2	liver
11	chr11:75475400-75477200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr11:75475600-75477000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr11:75475600-75477800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:75475600-75479200	Weak transcription	HMEC	breast
15	chr11:75475800-75478800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:75475800-75478800	Weak transcription	Liver	Liver
17	chr11:75476000-75477000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links