Variant report

Variant	rs2286379
Chromosome Location	chr12:1902164-1902165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1901917..1904602-chr12:2111317..2113842,2	MCF-7	breast:
2	chr12:1895293..1898168-chr12:1899496..1904929,5	MCF-7	breast:
3	chr12:1741431..1743986-chr12:1900425..1902270,2	MCF-7	breast:
4	chr12:1799303..1801733-chr12:1901384..1903711,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203593	Chromatin interaction
ENSG00000006831	Chromatin interaction
ENSG00000151065	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10128890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735003	0.82[CEU][hapmap]
rs10744552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10773991	0.82[CEU][hapmap]
rs10773997	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10773998	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10773999	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11614639	0.82[CEU][hapmap]
rs12300993	0.97[ASN][1000 genomes]
rs13219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476732	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2058111	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286383	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs2286384	0.82[CEU][hapmap]
rs3741971	0.91[JPT][hapmap]
rs4766415	0.81[CEU][hapmap]
rs4766417	0.93[ASN][1000 genomes]
rs4766418	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4766421	0.82[JPT][hapmap]
rs6489326	0.86[CEU][hapmap]
rs7294540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7294668	0.82[CEU][hapmap]
rs7300241	0.91[JPT][hapmap]
rs7315298	0.91[JPT][hapmap]
rs758168	0.83[CHB][hapmap];0.96[JPT][hapmap];0.80[ASN][1000 genomes]
rs9805049	0.85[CEU][hapmap];0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
8	nsv556996	chr12:1891372-1934920	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1824001	chr12:1896738-1951940	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv898592	chr12:1901485-1937801	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv898593	chr12:1901485-1962759	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood pressure (smoking interaction)	25189868	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2286379	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	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
2	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
3	chr12:1879000-1904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:1882600-1904800	Weak transcription	Stomach Mucosa	stomach
5	chr12:1885200-1904600	Weak transcription	Fetal Brain Male	brain
6	chr12:1885600-1902600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:1885800-1904000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:1886000-1904200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:1886000-1905000	Weak transcription	Fetal Brain Female	brain
10	chr12:1886200-1905400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:1887200-1905000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:1889200-1904800	Weak transcription	Right Atrium	heart
13	chr12:1889400-1904200	Weak transcription	Brain Germinal Matrix	brain
14	chr12:1889600-1904000	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:1889600-1905000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:1891200-1904200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:1891600-1903200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:1893200-1904800	Weak transcription	Hela-S3	cervix
19	chr12:1895600-1902600	Weak transcription	Ovary	ovary
20	chr12:1895600-1904600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:1895600-1905000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:1895600-1905000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:1896000-1902200	Weak transcription	Fetal Lung	lung
24	chr12:1896200-1904800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:1896200-1904800	Weak transcription	HSMMtube	muscle
26	chr12:1896200-1904800	Weak transcription	NHDF-Ad	bronchial
27	chr12:1896400-1904800	Weak transcription	Esophagus	oesophagus
28	chr12:1896600-1904800	Weak transcription	Pancreas	Pancrea
29	chr12:1896600-1905000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr12:1896600-1905000	Weak transcription	NH-A	brain
31	chr12:1896800-1904800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:1897000-1904800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:1897000-1905000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:1897200-1904600	Weak transcription	Placenta	Placenta
35	chr12:1897400-1902200	Weak transcription	Right Ventricle	heart
36	chr12:1897400-1902600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:1897400-1904800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:1897400-1904800	Weak transcription	NHLF	lung
39	chr12:1897400-1904800	Weak transcription	Osteobl	bone
40	chr12:1897400-1905000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:1897400-1905000	Weak transcription	HMEC	breast
42	chr12:1897600-1902200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:1897600-1902800	Weak transcription	Left Ventricle	heart
44	chr12:1897600-1902800	Weak transcription	Lung	lung
45	chr12:1897600-1903200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:1897600-1904600	Weak transcription	Colonic Mucosa	Colon
47	chr12:1897600-1904600	Weak transcription	Fetal Intestine Large	intestine
48	chr12:1897600-1904600	Weak transcription	Psoas Muscle	Psoas
49	chr12:1897600-1904800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:1897600-1904800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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