Variant report

Variant	rs1872167
Chromosome Location	chr11:47901269-47901270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11039387	0.91[ASN][1000 genomes]
rs11819979	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11820480	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16938631	0.84[ASW][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs17198607	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs17791016	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305982	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305983	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2869531	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2869532	0.85[ASN][1000 genomes]
rs4303192	0.83[EUR][1000 genomes]
rs4752791	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752871	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752872	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752877	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752879	0.98[ASN][1000 genomes]
rs57436966	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58357937	0.85[ASN][1000 genomes]
rs59205786	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59652089	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60515486	0.83[ASN][1000 genomes]
rs6485772	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6485774	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs6485783	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6485784	0.91[ASN][1000 genomes]
rs6485788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6485789	0.89[AFR][1000 genomes]
rs7120737	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7121264	0.86[ASN][1000 genomes]
rs7124949	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7924699	0.98[ASN][1000 genomes]
rs7927611	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7942031	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7946766	1.00[CEU][hapmap];0.94[TSI][hapmap]
rs7952204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[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	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1049835	chr11:47837089-47928822	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv541036	chr11:47837089-47928822	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1872167	ATG13	cis	parietal	SCAN
rs1872167	OR4C3	cis	parietal	SCAN
rs1872167	SLC35C1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47900600-47903200	Enhancers	Primary B cells from peripheral blood	blood
2	chr11:47900800-47901600	Enhancers	Spleen	Spleen
3	chr11:47900800-47901600	Flanking Active TSS	GM12878-XiMat	blood
4	chr11:47900800-47903200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr11:47900800-47903600	Enhancers	Primary B cells from cord blood	blood
6	chr11:47901000-47902600	Weak transcription	A549	lung
7	chr11:47901000-47903000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:47901000-47903600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:47901200-47902600	Enhancers	Adipose Nuclei	Adipose
10	chr11:47901200-47903200	Enhancers	Primary monocytes fromperipheralblood	blood

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