Variant report

Variant	rs10773988
Chromosome Location	chr12:1856181-1856182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1044471	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs10735003	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744551	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10773980	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10773982	0.80[JPT][hapmap]
rs10773989	0.89[CEU][hapmap];0.84[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10773991	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10848548	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848550	0.92[CEU][hapmap]
rs10848557	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10848561	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10848563	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10848565	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10848567	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10848571	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061971	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11612383	0.84[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs11614639	0.82[CEU][hapmap]
rs12316367	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068485	0.85[CEU][hapmap]
rs2068491	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2108642	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2190556	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286383	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2286384	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759374	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4140992	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4765843	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4765844	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4766415	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489326	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7138924	0.92[CEU][hapmap]
rs7294668	0.89[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7296521	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7955261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974422	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7974924	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7976827	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7978362	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978783	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9300298	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9739162	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9805049	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][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	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1816200-1857800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:1816200-1866400	Weak transcription	Esophagus	oesophagus
3	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
4	chr12:1817000-1856600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:1823000-1866600	Weak transcription	Gastric	stomach
6	chr12:1824000-1866600	Weak transcription	HSMM	muscle
7	chr12:1826000-1885400	Weak transcription	NH-A	brain
8	chr12:1831400-1857800	Weak transcription	Lung	lung
9	chr12:1837000-1861600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:1845600-1885200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:1847600-1857800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:1847600-1863800	Weak transcription	Ovary	ovary
13	chr12:1847600-1885200	Weak transcription	Right Atrium	heart
14	chr12:1849800-1868400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:1849800-1868800	Weak transcription	Pancreas	Pancrea
16	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
17	chr12:1850000-1856800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:1850000-1866600	Weak transcription	Fetal Lung	lung
19	chr12:1850200-1856600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr12:1850200-1865800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:1850200-1885200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:1850400-1856200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:1850400-1863400	Weak transcription	Fetal Stomach	stomach
24	chr12:1850400-1870400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
26	chr12:1850800-1863400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:1850800-1863400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:1850800-1885200	Weak transcription	Right Ventricle	heart
29	chr12:1851000-1856200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:1851000-1863400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:1851000-1866400	Weak transcription	NHLF	lung
32	chr12:1851200-1858000	Weak transcription	Osteobl	bone
33	chr12:1851400-1856400	Weak transcription	Hela-S3	cervix
34	chr12:1851400-1856600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:1851400-1857000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:1851400-1866600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr12:1851600-1856200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:1851600-1858000	Weak transcription	Psoas Muscle	Psoas
39	chr12:1851600-1863400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:1851600-1866400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:1851800-1863400	Weak transcription	Thymus	Thymus
42	chr12:1851800-1863600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:1851800-1876600	Weak transcription	Stomach Mucosa	stomach
44	chr12:1854000-1858800	ZNF genes & repeats	GM12878-XiMat	blood
45	chr12:1854400-1864400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:1854600-1856200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:1854600-1859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:1854600-1863400	Weak transcription	Adipose Nuclei	Adipose
49	chr12:1854600-1863400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:1854600-1870400	Weak transcription	HSMMtube	muscle

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