Variant report

Variant	rs2370055
Chromosome Location	chr12:1887698-1887699
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	chr12:1881087..1883067-chr12:1886344..1888819,2	K562	blood:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1029629	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10773986	0.89[AMR][1000 genomes]
rs10848551	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10848552	0.84[ASN][1000 genomes]
rs10848553	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10848558	0.83[AMR][1000 genomes]
rs10848569	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11061919	0.84[AMR][1000 genomes]
rs11061920	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11061921	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11061923	0.81[AMR][1000 genomes]
rs11061924	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11061925	0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11061927	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11061935	0.80[CHB][hapmap]
rs11061937	0.87[AMR][1000 genomes]
rs11061940	0.83[AMR][1000 genomes]
rs11061946	0.80[CHB][hapmap]
rs11061952	0.80[CHB][hapmap]
rs11061957	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11061962	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11061967	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11061968	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11061973	0.81[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs11061974	0.87[CEU][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1136213	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11832817	0.88[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12230440	0.80[CHB][hapmap]
rs12230579	0.88[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12231894	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12342	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12582624	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12810020	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12812707	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12813694	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12821401	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12828908	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12831353	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16928704	0.82[ASN][1000 genomes]
rs2058033	0.80[CHB][hapmap]
rs2058034	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2058035	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2240613	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2286385	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34375871	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3809266	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4766413	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6489320	0.84[ASN][1000 genomes]
rs6489323	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6489324	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66590925	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7132033	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7297509	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7313760	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7975826	0.84[AMR][1000 genomes]
rs7978818	0.83[AMR][1000 genomes]
rs929434	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS 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	32 gene(s)	inside rSNPs	diseases
4	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
6	nsv1038425	chr12:1857052-1902302	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
2	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
3	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
4	chr12:1857200-1892800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:1857200-1893400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:1862000-1894800	Weak transcription	Colonic Mucosa	Colon
7	chr12:1867000-1890200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:1867200-1888200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:1867200-1892600	Weak transcription	Spleen	Spleen
10	chr12:1867200-1893000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:1868200-1901800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:1870200-1892600	Weak transcription	Ovary	ovary
13	chr12:1878600-1897800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:1879000-1904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:1880600-1888400	Weak transcription	Fetal Stomach	stomach
16	chr12:1880600-1892200	Weak transcription	Fetal Intestine Small	intestine
17	chr12:1880600-1892200	Weak transcription	Gastric	stomach
18	chr12:1880600-1892200	Weak transcription	Lung	lung
19	chr12:1880600-1894600	Weak transcription	Esophagus	oesophagus
20	chr12:1881200-1889000	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:1881600-1897400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:1881600-1897600	Strong transcription	Dnd41	blood
23	chr12:1881600-1897800	Strong transcription	Fetal Thymus	thymus
24	chr12:1882000-1889000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:1882000-1898200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:1882400-1893000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:1882400-1896000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:1882600-1888200	Weak transcription	Thymus	Thymus
29	chr12:1882600-1888400	Weak transcription	Fetal Lung	lung
30	chr12:1882600-1889000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:1882600-1904800	Weak transcription	Stomach Mucosa	stomach
32	chr12:1883200-1889200	Enhancers	NHDF-Ad	bronchial
33	chr12:1883200-1889600	Weak transcription	Placenta	Placenta
34	chr12:1883400-1889200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:1883400-1890000	Enhancers	Brain Anterior Caudate	brain
36	chr12:1883800-1888000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:1883800-1888800	Weak transcription	Brain Germinal Matrix	brain
38	chr12:1884000-1888200	Enhancers	Brain Hippocampus Middle	brain
39	chr12:1885000-1888400	Strong transcription	HepG2	liver
40	chr12:1885200-1888400	Strong transcription	GM12878-XiMat	blood
41	chr12:1885200-1889600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr12:1885200-1904600	Weak transcription	Fetal Brain Male	brain
43	chr12:1885400-1892200	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:1885400-1897800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:1885400-1898000	Strong transcription	Primary T cells from cord blood	blood
46	chr12:1885600-1895200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:1885600-1897600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr12:1885600-1902600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:1885800-1888000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:1885800-1889600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links