Variant report

Variant	rs546463
Chromosome Location	chr11:104832347-104832348
allele	C/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	POLR2A	chr11:104831967-104832714	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
CASP4	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs473086	0.85[ASN][1000 genomes]
rs474866	0.84[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs501944	0.85[ASN][1000 genomes]
rs511149	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs518604	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs523104	0.93[JPT][hapmap]
rs537093	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs540813	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs552932	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs560891	0.97[ASN][1000 genomes]
rs564436	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577625	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs579408	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs608212	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609092	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs630003	0.85[ASN][1000 genomes]
rs658560	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs666695	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs666723	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672016	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686999	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046098	chr11:104207210-105003661	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv531430	chr11:104380924-105194452	Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv832255	chr11:104674918-104846961	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv898355	chr11:104730322-104897843	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1040784	chr11:104763797-104855878	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv468862	chr11:104774014-105243371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv556218	chr11:104774014-105243371	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv898356	chr11:104779195-104838471	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv3385159	chr11:104786549-105051555	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv1041081	chr11:104797775-104912458	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv1044970	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv541160	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104813800-104837200	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:104814000-104838200	Weak transcription	Fetal Kidney	kidney
3	chr11:104817800-104837000	Weak transcription	Right Ventricle	heart
4	chr11:104821200-104836000	Weak transcription	Gastric	stomach
5	chr11:104821800-104834400	Weak transcription	Thymus	Thymus
6	chr11:104821800-104836600	Weak transcription	Aorta	Aorta
7	chr11:104821800-104837400	Weak transcription	HSMMtube	muscle
8	chr11:104822000-104834200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr11:104822000-104836800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:104824400-104836000	Weak transcription	Psoas Muscle	Psoas
11	chr11:104825200-104834400	Weak transcription	Fetal Lung	lung
12	chr11:104825400-104832800	Weak transcription	Adipose Nuclei	Adipose
13	chr11:104825400-104836400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:104825400-104836600	Weak transcription	Left Ventricle	heart
15	chr11:104825400-104836800	Weak transcription	Esophagus	oesophagus
16	chr11:104825400-104837400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:104825400-104838200	Weak transcription	HSMM	muscle
18	chr11:104825600-104834200	Weak transcription	Fetal Thymus	thymus
19	chr11:104825600-104835800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:104825600-104836800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:104825800-104835800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:104825800-104836600	Weak transcription	HUVEC	blood vessel
23	chr11:104827200-104836000	Weak transcription	NHDF-Ad	bronchial
24	chr11:104827600-104832600	Weak transcription	Small Intestine	intestine
25	chr11:104827600-104836000	Weak transcription	HMEC	breast
26	chr11:104827800-104832400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:104827800-104834200	Weak transcription	Hela-S3	cervix
28	chr11:104829400-104837200	Weak transcription	GM12878-XiMat	blood
29	chr11:104829600-104836400	Weak transcription	Pancreas	Pancrea
30	chr11:104829800-104834000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr11:104830000-104832400	Weak transcription	Primary B cells from cord blood	blood
32	chr11:104830600-104835800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:104831000-104833400	Strong transcription	Placenta	Placenta
34	chr11:104831400-104833200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:104831400-104833800	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr11:104831600-104832600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:104831600-104833000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:104831600-104833000	Genic enhancers	Lung	lung
39	chr11:104831600-104833000	Strong transcription	NHLF	lung
40	chr11:104831600-104833400	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr11:104831600-104833400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:104831600-104836400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr11:104831600-104837000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr11:104831800-104832400	ZNF genes & repeats	Fetal Stomach	stomach
45	chr11:104831800-104832600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:104831800-104832600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:104831800-104832600	Strong transcription	Ovary	ovary
48	chr11:104831800-104832800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr11:104831800-104832800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:104831800-104833000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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