Variant report

Variant	rs2441956
Chromosome Location	chr11:57796009-57796010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr11:57795672-57797054	IMR90	lung:	n/a	n/a
2	POLR2A	chr11:57795946-57796356	SK-N-MC	brain:	n/a	n/a
3	MAZ	chr11:57795957-57796976	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
OR6Q1	TF binding region
RNU6-899P	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11229216	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229225	0.86[ASN][1000 genomes]
rs11229228	0.86[ASN][1000 genomes]
rs11229229	0.86[ASN][1000 genomes]
rs11229232	0.86[ASN][1000 genomes]
rs11229238	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11229240	0.82[CEU][hapmap];0.83[CHD][hapmap];0.89[TSI][hapmap]
rs11229246	0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs11229251	1.00[JPT][hapmap]
rs11229255	0.83[CHD][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs1447173	1.00[JPT][hapmap]
rs17537868	0.82[CEU][hapmap];0.91[CHD][hapmap];0.89[TSI][hapmap]
rs2441953	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2441957	0.90[YRI][hapmap]
rs2441971	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2513707	0.81[YRI][hapmap]
rs2514183	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2514205	0.82[CEU][hapmap];0.95[YRI][hapmap]
rs35157521	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3844134	0.94[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4938884	0.86[ASN][1000 genomes]
rs4939179	0.91[CHD][hapmap];0.82[TSI][hapmap]
rs7128492	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	esv2761678	chr11:57768288-57810886	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2441956	MS4A1	cis	parietal	SCAN
rs2441956	YPEL4	cis	multi-tissue	Pritchard
rs2441956	OR4D11	cis	parietal	SCAN
rs2441956	TIMM10	cis	parietal	SCAN
rs2441956	TIMM10	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57791200-57798200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr11:57792000-57811400	Weak transcription	Right Atrium	heart
3	chr11:57792400-57796800	Weak transcription	Esophagus	oesophagus
4	chr11:57792600-57796400	Weak transcription	HSMMtube	muscle
5	chr11:57792800-57796600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr11:57794400-57797000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:57794400-57797200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:57794400-57797800	Enhancers	NHLF	lung
9	chr11:57794600-57796200	Enhancers	HepG2	liver
10	chr11:57794600-57797000	Enhancers	Placenta	Placenta
11	chr11:57794600-57797000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr11:57794600-57797000	Enhancers	Osteobl	bone
13	chr11:57794600-57797400	Enhancers	Fetal Lung	lung
14	chr11:57794800-57797800	Enhancers	Adipose Nuclei	Adipose
15	chr11:57795000-57796600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:57795200-57797000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr11:57795400-57796200	Enhancers	Fetal Stomach	stomach
18	chr11:57795600-57796200	Enhancers	Spleen	Spleen
19	chr11:57795600-57797000	Enhancers	Duodenum Mucosa	Duodenum
20	chr11:57795800-57796600	Weak transcription	Colonic Mucosa	Colon
21	chr11:57795800-57796600	Weak transcription	Lung	lung
22	chr11:57796000-57796200	Enhancers	Aorta	Aorta
23	chr11:57796000-57796400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:57796000-57796400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:57796000-57796400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:57796000-57796400	Weak transcription	Left Ventricle	heart
27	chr11:57796000-57796400	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links