Variant report

Variant	rs10771486
Chromosome Location	chr12:29320763-29320764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29274504..29277462-chr12:29319528..29321413,2	K562	blood:
2	chr12:29300930..29303778-chr12:29318303..29322829,4	K562	blood:

Variant related genes	Relation type
ENSG00000257258	Chromatin interaction
ENSG00000064763	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10743645	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743647	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10743648	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10743649	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10771489	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771492	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10771494	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843343	0.88[EUR][1000 genomes]
rs11050084	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050098	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050099	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050104	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050110	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050112	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050114	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12310732	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319200	0.91[CEU][hapmap]
rs12366549	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1496218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1561132	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1826800	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1845819	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1908690	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1908691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2349974	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4105125	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4105126	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4105127	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4105128	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4141943	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4141945	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4323913	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4536271	0.93[ASN][1000 genomes]
rs4930856	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4930857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930858	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930859	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4931158	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931162	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4931163	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4931165	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60287933	0.98[ASN][1000 genomes]
rs6487778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487783	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71453727	1.00[ASN][1000 genomes]
rs7294355	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7297542	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7309041	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7309881	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73265795	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7968949	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975191	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7980923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs924105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924107	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs924109	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs958478	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29306600-29324600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:29306800-29324400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:29308400-29324000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:29308400-29324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:29316200-29324200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr12:29316200-29324400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:29316800-29323800	Enhancers	Fetal Intestine Large	intestine
8	chr12:29317000-29320800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:29317000-29324000	Enhancers	Fetal Intestine Small	intestine
10	chr12:29317600-29322000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:29317600-29324400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:29317600-29324400	Weak transcription	Lung	lung
13	chr12:29317600-29340800	Weak transcription	Left Ventricle	heart
14	chr12:29317800-29321000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:29317800-29321600	Weak transcription	Spleen	Spleen
16	chr12:29317800-29322200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr12:29317800-29323000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr12:29317800-29324000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:29317800-29324400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr12:29317800-29324400	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:29317800-29324400	Weak transcription	Fetal Stomach	stomach
22	chr12:29317800-29326800	Weak transcription	Primary T cells from cord blood	blood
23	chr12:29318000-29323000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr12:29318200-29322600	Weak transcription	Adipose Nuclei	Adipose
25	chr12:29318200-29324200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:29318200-29324200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:29318200-29324400	Weak transcription	Dnd41	blood
28	chr12:29318200-29326200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:29318400-29321200	Weak transcription	Fetal Lung	lung
30	chr12:29318400-29322600	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr12:29318400-29324600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:29318400-29329600	Weak transcription	NHLF	lung
33	chr12:29318800-29324000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:29319000-29322200	Weak transcription	HUVEC	blood vessel
35	chr12:29319000-29322600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:29319600-29321400	Enhancers	Colonic Mucosa	Colon
37	chr12:29319800-29321400	Enhancers	Stomach Mucosa	stomach
38	chr12:29320200-29321200	Weak transcription	Small Intestine	intestine
39	chr12:29320200-29322200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:29320200-29324400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:29320400-29320800	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr12:29320600-29321200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr12:29320600-29321200	Enhancers	Rectal Smooth Muscle	rectum
44	chr12:29320600-29321400	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr12:29320600-29322200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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