Variant report

Variant	rs12231804
Chromosome Location	chr12:25229033-25229034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11047803	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11047806	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047812	1.00[CEU][hapmap];1.00[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]
rs12229033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230333	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12230689	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12426684	1.00[JPT][hapmap]
rs17326292	1.00[CEU][hapmap];1.00[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]
rs17326622	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4963601	1.00[CEU][hapmap];1.00[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:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25209400-25264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:25210000-25262800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:25212000-25250800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:25214400-25245600	Weak transcription	Ovary	ovary
5	chr12:25214400-25251800	Weak transcription	Fetal Intestine Large	intestine
6	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:25218600-25239200	Weak transcription	Fetal Intestine Small	intestine
8	chr12:25221600-25229200	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr12:25221600-25235800	Weak transcription	Liver	Liver
10	chr12:25222400-25236000	Weak transcription	Adipose Nuclei	Adipose
11	chr12:25222800-25232200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:25223000-25238000	Weak transcription	Spleen	Spleen
13	chr12:25223400-25232200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:25223400-25235400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:25223600-25232000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:25223600-25232200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:25223600-25232200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:25224000-25232200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:25224600-25230600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:25224600-25241600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:25225400-25232200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:25225400-25237800	Weak transcription	Lung	lung
23	chr12:25226000-25232000	Weak transcription	Dnd41	blood
24	chr12:25226600-25230400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr12:25226600-25232000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:25226600-25232200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:25226800-25230800	Weak transcription	Primary T cells from cord blood	blood
28	chr12:25227400-25251000	Weak transcription	Pancreas	Pancrea
29	chr12:25227600-25231800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr12:25227800-25229200	Enhancers	GM12878-XiMat	blood
31	chr12:25228000-25230600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:25228000-25230600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:25228000-25232000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:25228200-25233000	Strong transcription	Primary B cells from cord blood	blood
35	chr12:25228400-25229200	Enhancers	Thymus	Thymus
36	chr12:25228400-25241200	Weak transcription	Stomach Mucosa	stomach
37	chr12:25228800-25236200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:25229000-25229800	Weak transcription	Fetal Thymus	thymus
39	chr12:25229000-25232000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:25229000-25237800	Weak transcription	Esophagus	oesophagus
41	chr12:25229000-25253000	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links