Variant report

Variant	rs12507739
Chromosome Location	chr4:54352768-54352769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54352104..54354380-chr4:54439220..54441947,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173966	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10000746	0.88[CHB][hapmap]
rs10001201	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10005424	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10007903	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10011259	0.81[CEU][hapmap]
rs10011394	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10021541	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10028142	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10032903	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1021099	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11133276	0.90[CEU][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11722866	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11723755	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11725230	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11734039	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11734681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944047	0.81[GIH][hapmap]
rs11947256	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12507563	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12508701	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12511088	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12511253	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12642403	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12649718	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12651390	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap]
rs13150384	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1471597	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1481819	0.82[CEU][hapmap]
rs1481824	0.82[CEU][hapmap]
rs1531748	0.86[CEU][hapmap]
rs17082893	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17082923	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17520800	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2090117	0.82[CEU][hapmap]
rs2271558	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271559	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2412447	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412488	0.82[CEU][hapmap]
rs28414913	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28459503	0.83[ASN][1000 genomes]
rs35089837	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35499169	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35978987	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36011216	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765158	0.82[CEU][hapmap]
rs3811785	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4864760	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4864767	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56998298	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57297394	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6554104	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6554105	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6554106	0.82[CEU][hapmap]
rs6554109	0.81[GIH][hapmap]
rs6818788	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6822201	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6825364	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6828559	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs6832626	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6833766	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6835629	0.81[GIH][hapmap]
rs6838260	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6839922	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6840343	0.87[CEU][hapmap];0.91[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6840530	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6843529	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6848887	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7655975	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7682199	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7686876	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7688853	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7689981	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7690908	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7691578	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7691892	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7697622	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7698792	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs931181	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs931182	0.82[CEU][hapmap]
rs9312639	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs9995284	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9996883	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12507739	EXOC1	cis	cerebellum	SCAN
rs12507739	ZNF585A	cis	Frontal Cortex	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54320000-54353200	Weak transcription	Gastric	stomach
2	chr4:54327800-54362200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:54328200-54362000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:54328400-54362000	Weak transcription	Brain Angular Gyrus	brain
5	chr4:54329600-54373600	Weak transcription	Brain Germinal Matrix	brain
6	chr4:54329800-54374000	Weak transcription	Left Ventricle	heart
7	chr4:54333000-54363600	Weak transcription	Aorta	Aorta
8	chr4:54333000-54374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:54342800-54360600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
11	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
12	chr4:54343400-54363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:54343600-54364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:54345800-54355400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:54346000-54356400	Weak transcription	HSMMtube	muscle
16	chr4:54346400-54374000	Weak transcription	Right Ventricle	heart
17	chr4:54347600-54401800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:54347800-54355000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr4:54348000-54353400	Weak transcription	Pancreas	Pancrea
20	chr4:54348000-54355600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:54348000-54362200	Weak transcription	Fetal Intestine Large	intestine
22	chr4:54348200-54359600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:54349000-54360000	Weak transcription	Liver	Liver
24	chr4:54350000-54353400	Enhancers	Ovary	ovary
25	chr4:54350400-54355200	Weak transcription	HMEC	breast
26	chr4:54351400-54355000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:54351600-54353000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:54351600-54355000	Weak transcription	Osteobl	bone
29	chr4:54352000-54355000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:54352200-54352800	Genic enhancers	Esophagus	oesophagus
31	chr4:54352200-54352800	Strong transcription	Fetal Intestine Small	intestine
32	chr4:54352200-54354600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:54352400-54354400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:54352600-54352800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:54352600-54355200	Enhancers	Fetal Brain Male	brain
36	chr4:54352600-54356800	Strong transcription	Placenta	Placenta

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