Variant report

Variant	rs963140
Chromosome Location	chr1:67037576-67037577
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10493411	0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs10789211	0.81[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10889629	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11208907	0.91[ASN][1000 genomes]
rs11208908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208910	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11208916	0.84[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11208924	0.84[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11208930	0.85[JPT][hapmap]
rs11208937	0.88[JPT][hapmap]
rs1156618	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12023176	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12034344	1.00[ASN][1000 genomes]
rs12039282	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12041930	0.84[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12046520	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12117649	0.85[CEU][hapmap]
rs12565798	0.91[ASN][1000 genomes]
rs12567556	1.00[ASN][1000 genomes]
rs1373909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17129124	0.85[YRI][hapmap]
rs1925342	0.94[JPT][hapmap]
rs2312153	0.90[ASN][1000 genomes]
rs3795531	0.94[ASN][1000 genomes]
rs4655498	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588209	0.81[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs6588214	0.94[JPT][hapmap]
rs6680968	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686606	0.81[JPT][hapmap]
rs6687137	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701907	0.94[JPT][hapmap]
rs6701988	1.00[ASN][1000 genomes]
rs72918447	0.81[ASN][1000 genomes]
rs7512692	0.85[ASN][1000 genomes]
rs7519639	0.91[ASN][1000 genomes]
rs7525509	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526812	0.94[JPT][hapmap]
rs7535076	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7537440	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7547794	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7547857	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7547866	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551301	0.81[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs963141	0.89[ASW][hapmap];0.82[YRI][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs963140	TCTEX1D1	cis	parietal	SCAN
rs963140	TCTEX1D1	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67029200-67042600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:67029400-67040800	Weak transcription	Brain Anterior Caudate	brain
3	chr1:67029400-67041400	Weak transcription	Left Ventricle	heart
4	chr1:67029600-67041400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:67029600-67041600	Weak transcription	Aorta	Aorta
6	chr1:67029800-67040200	Weak transcription	Fetal Heart	heart
7	chr1:67032000-67041400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:67035600-67038200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:67035600-67038200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:67035600-67038400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:67035600-67038400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:67035600-67038400	Enhancers	NHEK	skin
13	chr1:67035600-67038600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:67035800-67038200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:67035800-67038400	Enhancers	NHDF-Ad	bronchial
16	chr1:67036000-67038400	Enhancers	HMEC	breast
17	chr1:67036000-67038400	Enhancers	NHLF	lung
18	chr1:67036000-67039200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:67036200-67038000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:67036200-67038200	Enhancers	Osteobl	bone
21	chr1:67037000-67038000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:67037000-67038400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:67037000-67040800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:67037000-67041600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:67037400-67038000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:67037400-67038000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:67037400-67038000	Enhancers	Hela-S3	cervix
28	chr1:67037400-67038000	Enhancers	HSMM	muscle
29	chr1:67037400-67038200	Enhancers	NH-A	brain

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