Variant report

Variant	rs11150612
Chromosome Location	chr16:31357760-31357761
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	chr16:31190461..31191992-chr16:31356554..31358411,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10747210	0.97[ASN][1000 genomes]
rs10782004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1106398	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11150610	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.89[ASN][1000 genomes]
rs11150611	0.98[ASN][1000 genomes]
rs11150613	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11150614	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11150616	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11150617	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11150619	0.85[CEU][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1143682	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11574630	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11574631	0.93[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11574639	0.83[ASN][1000 genomes]
rs11641202	0.90[CHD][hapmap];0.86[ASN][1000 genomes]
rs11642120	0.86[ASN][1000 genomes]
rs11645917	0.99[ASN][1000 genomes]
rs11859274	0.99[ASN][1000 genomes]
rs11863627	0.85[ASN][1000 genomes]
rs12444713	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12597154	0.89[ASN][1000 genomes]
rs12600286	0.92[ASN][1000 genomes]
rs12923297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12935192	0.99[ASN][1000 genomes]
rs13332545	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs13338928	0.88[ASN][1000 genomes]
rs2230429	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2359661	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs28372932	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3087796	0.92[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs36100148	0.91[ASN][1000 genomes]
rs3925074	0.94[ASN][1000 genomes]
rs3925075	0.94[ASN][1000 genomes]
rs4075052	0.93[ASN][1000 genomes]
rs4077810	0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs41440449	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4261553	0.93[ASN][1000 genomes]
rs4280256	0.80[ASN][1000 genomes]
rs4359460	0.93[ASN][1000 genomes]
rs4411512	0.93[ASN][1000 genomes]
rs4448960	0.94[ASN][1000 genomes]
rs4450409	0.85[ASN][1000 genomes]
rs4459557	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4493054	0.97[ASN][1000 genomes]
rs4506917	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs4594268	0.86[ASN][1000 genomes]
rs4597342	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4608351	0.93[ASN][1000 genomes]
rs4889543	0.89[ASN][1000 genomes]
rs4889647	0.87[ASN][1000 genomes]
rs4889649	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55742763	0.89[ASN][1000 genomes]
rs55912556	0.85[ASN][1000 genomes]
rs56392848	0.98[ASN][1000 genomes]
rs57202326	0.86[ASN][1000 genomes]
rs59338016	0.89[ASN][1000 genomes]
rs61194152	0.94[ASN][1000 genomes]
rs62051517	0.91[ASN][1000 genomes]
rs7190997	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7192161	0.87[ASN][1000 genomes]
rs7192375	0.88[ASN][1000 genomes]
rs7195915	0.91[ASN][1000 genomes]
rs7195945	0.91[ASN][1000 genomes]
rs7206295	0.93[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7499192	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7501207	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8048583	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs8052324	0.87[ASN][1000 genomes]
rs8058882	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8060268	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs8062159	0.86[ASN][1000 genomes]
rs9673398	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9673404	0.92[ASN][1000 genomes]
rs9673405	0.94[ASN][1000 genomes]
rs9673519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9673522	0.94[ASN][1000 genomes]
rs9674009	0.94[ASN][1000 genomes]
rs9888907	0.93[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	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
4	nsv1058992	chr16:31337455-31414881	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv542902	chr16:31337455-31414881	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1061980	chr16:31338462-31415471	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11150612	ITGAX	cis	cerebellum	SCAN
rs11150612	SULT1A2	cis	cerebellum	SCAN
rs11150612	PRSS36	cis	parietal	SCAN
rs11150612	ITGAM	cis	lymphoblastoid	seeQTL
rs11150612	PRSS8	cis	parietal	SCAN
rs11150612	TBX6	cis	parietal	SCAN
rs11150612	PYCARD	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31343000-31400800	Weak transcription	Right Atrium	heart
2	chr16:31355600-31365600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:31356400-31359000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr16:31356400-31361600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr16:31356600-31358600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr16:31356600-31358800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:31356600-31359400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr16:31356600-31359600	Weak transcription	Spleen	Spleen
9	chr16:31356600-31363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr16:31356800-31358000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr16:31357000-31358000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr16:31357000-31358800	Weak transcription	GM12878-XiMat	blood
13	chr16:31357000-31359600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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