Variant report

Variant	rs1860049
Chromosome Location	chr12:1884345-1884346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1805243..1808157-chr12:1884262..1886640,2	MCF-7	breast:
2	chr12:1797794..1800188-chr12:1882818..1885035,2	MCF-7	breast:
3	chr12:1799342..1802388-chr12:1883886..1887202,3	MCF-7	breast:
4	chr12:1883679..1886349-chr12:1898971..1901942,2	MCF-7	breast:
5	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: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11061904	1.00[EUR][1000 genomes]
rs2041059	1.00[EUR][1000 genomes]
rs2108398	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2369974	0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2370054	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35510932	1.00[EUR][1000 genomes]
rs4765838	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4766411	1.00[EUR][1000 genomes]
rs4766420	1.00[EUR][1000 genomes]
rs56369812	1.00[EUR][1000 genomes]
rs6489321	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6489325	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7133749	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7135229	1.00[EUR][1000 genomes]
rs7136278	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs7297878	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7304843	0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7308757	1.00[EUR][1000 genomes]
rs7314133	1.00[EUR][1000 genomes]
rs74061311	1.00[EUR][1000 genomes]
rs74061331	1.00[EUR][1000 genomes]
rs74061332	1.00[EUR][1000 genomes]
rs758026	1.00[EUR][1000 genomes]
rs758027	0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs758169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7957003	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7962777	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7964434	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv973980	chr12:1879789-1884543	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv2586584	chr12:1883343-1884771	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 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	chr12:1845600-1885200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:1847600-1885200	Weak transcription	Right Atrium	heart
5	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
6	chr12:1850200-1885200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
8	chr12:1850800-1885200	Weak transcription	Right Ventricle	heart
9	chr12:1857200-1892800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:1857200-1893400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:1862000-1894800	Weak transcription	Colonic Mucosa	Colon
12	chr12:1864800-1885400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:1865000-1885200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:1867000-1890200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:1867200-1885600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:1867200-1888200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:1867200-1892600	Weak transcription	Spleen	Spleen
18	chr12:1867200-1893000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:1867600-1886800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:1867800-1885000	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:1868200-1901800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:1868400-1887000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:1868800-1885000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:1869000-1884600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:1869200-1884400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:1870200-1892600	Weak transcription	Ovary	ovary
27	chr12:1871000-1885400	Weak transcription	HSMMtube	muscle
28	chr12:1875600-1885000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:1875600-1885200	Weak transcription	HMEC	breast
30	chr12:1875600-1885400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr12:1878600-1897800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:1879000-1904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:1879200-1885400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr12:1879400-1884400	Weak transcription	Fetal Brain Male	brain
35	chr12:1879400-1884400	Weak transcription	Fetal Brain Female	brain
36	chr12:1879400-1885000	Weak transcription	Osteobl	bone
37	chr12:1879400-1885200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:1879400-1885400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:1879600-1885000	Weak transcription	NHEK	skin
40	chr12:1879600-1885200	Weak transcription	Hela-S3	cervix
41	chr12:1880400-1885400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:1880600-1884600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:1880600-1885200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:1880600-1885200	Weak transcription	Left Ventricle	heart
45	chr12:1880600-1885400	Weak transcription	Pancreas	Pancrea
46	chr12:1880600-1888400	Weak transcription	Fetal Stomach	stomach
47	chr12:1880600-1892200	Weak transcription	Fetal Intestine Small	intestine
48	chr12:1880600-1892200	Weak transcription	Gastric	stomach
49	chr12:1880600-1892200	Weak transcription	Lung	lung
50	chr12:1880600-1894600	Weak transcription	Esophagus	oesophagus

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