Variant report

Variant	rs10773991
Chromosome Location	chr12:1885306-1885307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1880016..1882421-chr12:1884349..1886060,2	K562	blood:
2	chr12:1805243..1808157-chr12:1884262..1886640,2	MCF-7	breast:
3	chr12:1884779..1887439-chr12:1888065..1890449,2	K562	blood:
4	chr12:1884663..1886181-chr12:1889838..1891641,2	MCF-7	breast:
5	chr12:1799342..1802388-chr12:1883886..1887202,3	MCF-7	breast:
6	chr12:1883679..1886349-chr12:1898971..1901942,2	MCF-7	breast:
7	chr12:1874405..1877121-chr12:1883509..1886504,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction
ENSG00000271500	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10128890	0.81[CEU][hapmap]
rs1044471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1044825	0.81[CEU][hapmap]
rs10735003	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10744551	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10744552	0.81[CEU][hapmap]
rs10773980	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10773988	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]
rs10773989	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes]
rs10848548	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10848550	0.88[CEU][hapmap]
rs10848557	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10848561	0.85[ASN][1000 genomes]
rs10848563	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10848565	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10848567	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10848571	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061971	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612383	0.82[CHB][hapmap]
rs11614639	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs12316367	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13219	0.81[CEU][hapmap]
rs2068485	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2068491	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108642	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2190556	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286379	0.82[CEU][hapmap]
rs2286383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759374	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140992	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4765843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765844	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489326	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138924	0.89[CEU][hapmap]
rs7294540	0.81[CEU][hapmap]
rs7294668	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296521	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7955261	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7974422	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974924	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976827	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978362	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7978783	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9300298	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9739162	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9805049	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[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	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
2	chr12:1826000-1885400	Weak transcription	NH-A	brain
3	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
4	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
5	chr12:1857200-1892800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:1857200-1893400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:1862000-1894800	Weak transcription	Colonic Mucosa	Colon
8	chr12:1864800-1885400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:1867000-1890200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:1867200-1885600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:1867200-1888200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:1867200-1892600	Weak transcription	Spleen	Spleen
13	chr12:1867200-1893000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr12:1867600-1886800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:1868200-1901800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:1868400-1887000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:1870200-1892600	Weak transcription	Ovary	ovary
18	chr12:1871000-1885400	Weak transcription	HSMMtube	muscle
19	chr12:1875600-1885400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr12:1878600-1897800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr12:1879000-1904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:1879200-1885400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:1879400-1885400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:1880400-1885400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:1880600-1885400	Weak transcription	Pancreas	Pancrea
26	chr12:1880600-1888400	Weak transcription	Fetal Stomach	stomach
27	chr12:1880600-1892200	Weak transcription	Fetal Intestine Small	intestine
28	chr12:1880600-1892200	Weak transcription	Gastric	stomach
29	chr12:1880600-1892200	Weak transcription	Lung	lung
30	chr12:1880600-1894600	Weak transcription	Esophagus	oesophagus
31	chr12:1881200-1889000	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:1881600-1885800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:1881600-1897400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr12:1881600-1897600	Strong transcription	Dnd41	blood
35	chr12:1881600-1897800	Strong transcription	Fetal Thymus	thymus
36	chr12:1881800-1886400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:1882000-1886200	Strong transcription	Primary B cells from cord blood	blood
38	chr12:1882000-1889000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr12:1882000-1898200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:1882400-1886000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:1882400-1893000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:1882400-1896000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr12:1882600-1885400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:1882600-1886800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr12:1882600-1888200	Weak transcription	Thymus	Thymus
46	chr12:1882600-1888400	Weak transcription	Fetal Lung	lung
47	chr12:1882600-1889000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr12:1882600-1904800	Weak transcription	Stomach Mucosa	stomach
49	chr12:1883000-1885400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:1883000-1886800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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