Variant report

Variant	rs7512401
Chromosome Location	chr1:67157448-67157449
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1014778	0.84[CEU][hapmap]
rs10789216	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889633	0.80[CEU][hapmap]
rs10889647	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10889649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11208934	0.84[CEU][hapmap]
rs11208939	0.84[CEU][hapmap]
rs11208944	0.82[CHD][hapmap]
rs11208945	0.82[CHD][hapmap]
rs11208948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208951	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1160675	0.80[CEU][hapmap]
rs11811699	0.92[CEU][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12063436	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12119578	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12128857	0.84[CEU][hapmap]
rs12138266	0.88[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1325268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408852	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1445572	0.80[CEU][hapmap]
rs1498354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1547644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016093	0.83[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs2181625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274987	0.83[AMR][1000 genomes]
rs2312573	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3738167	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4143026	0.84[CEU][hapmap]
rs473470	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs485122	0.83[ASN][1000 genomes]
rs487833	0.81[JPT][hapmap]
rs489300	0.95[ASN][1000 genomes]
rs512691	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs524204	0.81[JPT][hapmap]
rs553729	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs562348	0.80[ASN][1000 genomes]
rs650202	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs657808	0.83[CHD][hapmap]
rs6588216	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6656461	0.84[CEU][hapmap]
rs6656705	0.84[CEU][hapmap]
rs6659325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663604	0.84[AMR][1000 genomes]
rs6666600	0.84[CEU][hapmap]
rs6679379	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6696973	0.80[CEU][hapmap]
rs6697365	0.80[CEU][hapmap]
rs678253	0.81[JPT][hapmap]
rs682896	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs693956	0.86[CHD][hapmap];0.87[JPT][hapmap]
rs7524680	0.84[CEU][hapmap]
rs7528346	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7537454	0.80[CEU][hapmap]
rs7541249	0.83[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs963141	0.80[CEU][hapmap]
rs9659684	0.84[CEU][hapmap]
rs9660797	0.84[CEU][hapmap]
rs9988481	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7512401	ATP2A1	trans	cerebellum	SCAN
rs7512401	TCTEX1D1	cis	cerebellum	SCAN
rs7512401	TCTEX1D1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67140600-67161200	Weak transcription	Esophagus	oesophagus
2	chr1:67144600-67160800	Weak transcription	Lung	lung
3	chr1:67149200-67161000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:67152000-67162800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:67152800-67159800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:67153400-67161200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:67155200-67158200	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr1:67155600-67159600	Weak transcription	NHDF-Ad	bronchial
9	chr1:67155600-67167400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:67155800-67158000	Weak transcription	NH-A	brain
11	chr1:67155800-67158200	Weak transcription	Brain Angular Gyrus	brain
12	chr1:67155800-67164600	Weak transcription	Fetal Brain Male	brain
13	chr1:67155800-67168200	Weak transcription	Fetal Heart	heart
14	chr1:67155800-67177200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:67156000-67158000	Weak transcription	Left Ventricle	heart
16	chr1:67156000-67159600	Weak transcription	NHLF	lung
17	chr1:67156000-67161400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:67156000-67177200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:67156200-67158000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:67156200-67159400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:67156200-67164400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:67156600-67158200	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:67156800-67157600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:67156800-67166800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:67156800-67167600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:67156800-67191400	Weak transcription	Fetal Brain Female	brain
27	chr1:67157000-67160800	Weak transcription	Aorta	Aorta
28	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
29	chr1:67157200-67158000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:67157200-67160200	Weak transcription	Fetal Intestine Small	intestine
31	chr1:67157200-67160600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:67157200-67160800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:67157200-67160800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:67157200-67189600	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:67157400-67162200	Weak transcription	Fetal Intestine Large	intestine
36	chr1:67157400-67191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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