Variant report

Variant	rs2286385
Chromosome Location	chr12:1890589-1890590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1799392..1801611-chr12:1889513..1892415,2	MCF-7	breast:
2	chr12:1797404..1801222-chr12:1889533..1893167,4	MCF-7	breast:
3	chr12:1884663..1886181-chr12:1889838..1891641,2	MCF-7	breast:
4	chr12:1769289..1772614-chr12:1889825..1893235,5	K562	blood:
5	chr12:1890411..1894703-chr12:1895509..1898196,4	K562	blood:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction
ENSG00000266043	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10773982	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10773986	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773989	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10848553	0.83[AMR][1000 genomes]
rs10848558	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10848569	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11061919	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11061920	0.83[AMR][1000 genomes]
rs11061921	0.83[AMR][1000 genomes]
rs11061923	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11061924	0.83[AMR][1000 genomes]
rs11061927	0.83[AMR][1000 genomes]
rs11061937	0.87[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11061940	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11061957	0.86[AMR][1000 genomes]
rs11061962	0.88[AMR][1000 genomes]
rs11061968	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11061974	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1136213	0.83[AMR][1000 genomes]
rs11614639	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11832817	0.86[AMR][1000 genomes]
rs12230579	0.86[AMR][1000 genomes]
rs12231894	0.88[AMR][1000 genomes]
rs12342	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582624	0.88[AMR][1000 genomes]
rs12810020	0.88[AMR][1000 genomes]
rs12812707	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12813694	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12828908	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12831353	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2058034	0.83[AMR][1000 genomes]
rs2058035	0.83[AMR][1000 genomes]
rs2068485	0.89[ASN][1000 genomes]
rs2240613	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370055	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34375871	0.88[AMR][1000 genomes]
rs3809266	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766413	0.82[AMR][1000 genomes]
rs6489323	0.84[AMR][1000 genomes]
rs6489324	0.88[AMR][1000 genomes]
rs66590925	0.88[AMR][1000 genomes]
rs7132033	0.83[AMR][1000 genomes]
rs7297509	0.88[AMR][1000 genomes]
rs7313760	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7975826	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7978818	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs929434	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv430442	chr12:1889823-1982151	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2286385	CACNA2D4	cis	multi-tissue	Pritchard

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	chr12:1867200-1892600	Weak transcription	Spleen	Spleen
8	chr12:1867200-1893000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:1868200-1901800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:1870200-1892600	Weak transcription	Ovary	ovary
11	chr12:1878600-1897800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:1879000-1904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:1880600-1892200	Weak transcription	Fetal Intestine Small	intestine
14	chr12:1880600-1892200	Weak transcription	Gastric	stomach
15	chr12:1880600-1892200	Weak transcription	Lung	lung
16	chr12:1880600-1894600	Weak transcription	Esophagus	oesophagus
17	chr12:1881600-1897400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr12:1881600-1897600	Strong transcription	Dnd41	blood
19	chr12:1881600-1897800	Strong transcription	Fetal Thymus	thymus
20	chr12:1882000-1898200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:1882400-1893000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:1882400-1896000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:1882600-1904800	Weak transcription	Stomach Mucosa	stomach
24	chr12:1885200-1904600	Weak transcription	Fetal Brain Male	brain
25	chr12:1885400-1892200	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:1885400-1897800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:1885400-1898000	Strong transcription	Primary T cells from cord blood	blood
28	chr12:1885600-1895200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:1885600-1897600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr12:1885600-1902600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:1885800-1890600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr12:1885800-1896600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:1885800-1904000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:1886000-1890800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:1886000-1890800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:1886000-1890800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:1886000-1890800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:1886000-1890800	Weak transcription	Right Ventricle	heart
39	chr12:1886000-1892600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:1886000-1892800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:1886000-1894600	Weak transcription	Pancreas	Pancrea
42	chr12:1886000-1904200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:1886000-1905000	Weak transcription	Fetal Brain Female	brain
44	chr12:1886200-1890800	Weak transcription	HSMMtube	muscle
45	chr12:1886200-1897800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:1886200-1905400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:1886800-1891600	Enhancers	Brain Angular Gyrus	brain
48	chr12:1886800-1897200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr12:1886800-1897600	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:1886800-1897800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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