Variant report

Variant	rs11051879
Chromosome Location	chr12:9758119-9758120
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10743789	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10771926	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771927	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771929	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771930	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771935	0.85[ASN][1000 genomes]
rs10771936	0.90[ASN][1000 genomes]
rs10771947	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10772001	0.85[YRI][hapmap]
rs10844160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844161	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844191	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10844196	0.82[ASN][1000 genomes]
rs10844206	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844225	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844233	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844269	0.84[ASN][1000 genomes]
rs11051877	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11051959	0.90[ASN][1000 genomes]
rs11052008	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11052013	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11052027	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11052031	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12301481	0.89[ASN][1000 genomes]
rs12308360	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12321613	0.90[ASN][1000 genomes]
rs12580472	0.96[ASN][1000 genomes]
rs12818361	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1529418	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1529419	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1863876	0.89[ASN][1000 genomes]
rs1987426	0.89[ASN][1000 genomes]
rs2401386	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs35721310	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4486710	0.87[ASN][1000 genomes]
rs4763655	0.83[TSI][hapmap]
rs4763675	0.91[ASN][1000 genomes]
rs4763678	0.83[ASN][1000 genomes]
rs4763717	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs5023032	1.00[ASW][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60416399	0.89[ASN][1000 genomes]
rs6488042	0.83[ASN][1000 genomes]
rs6488054	0.90[ASN][1000 genomes]
rs66927586	0.89[ASN][1000 genomes]
rs7132715	0.84[ASN][1000 genomes]
rs7138619	0.93[ASN][1000 genomes]
rs72656628	0.87[ASN][1000 genomes]
rs72656629	0.81[ASN][1000 genomes]
rs7301291	0.89[ASN][1000 genomes]
rs7302021	0.82[ASN][1000 genomes]
rs7310367	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7311954	0.89[ASN][1000 genomes]
rs7314188	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7954289	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv8909	chr12:9754887-9758694	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases
10	esv3503696	chr12:9756816-9758313	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
11	esv3503685	chr12:9756892-9758291	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases
12	esv3449854	chr12:9756944-9758292	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases
13	esv3503992	chr12:9756955-9758270	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers	n/a	n/a	inside rSNPs	diseases
14	esv3503993	chr12:9756955-9758270	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers	n/a	n/a	inside rSNPs	diseases
15	esv3503707	chr12:9756980-9758243	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11051879	GSG1	cis	cerebellum	SCAN
rs11051879	CLEC2D	cis	multi-tissue	Pritchard
rs11051879	DCAL1	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9734400-9763000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:9736000-9760200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:9738200-9759600	Weak transcription	Primary T cells from cord blood	blood
4	chr12:9746000-9760000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:9750000-9759600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:9755800-9771200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:9757000-9758200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:9757000-9758400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:9757200-9760600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:9757200-9763000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:9757800-9759200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:9758000-9758400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr12:9758000-9760400	Active TSS	Primary T cells fromperipheralblood	blood
14	chr12:9758000-9760600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links