Variant report

Variant	rs6588216
Chromosome Location	chr1:67145847-67145848
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1014778	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs10789216	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10889633	0.86[CEU][hapmap]
rs10889639	0.84[JPT][hapmap]
rs10889649	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11208934	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs11208939	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs11208944	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11208945	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11208948	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11208951	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1160675	0.87[CEU][hapmap]
rs11811699	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12031054	0.83[JPT][hapmap]
rs12043460	0.96[ASN][1000 genomes]
rs12063436	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12128857	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs12138266	0.86[CEU][hapmap]
rs12402709	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1325268	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1359461	0.85[JPT][hapmap]
rs1445572	0.87[CEU][hapmap]
rs1498354	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1547644	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16844	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1838652	0.87[CEU][hapmap]
rs2016093	0.82[CEU][hapmap]
rs2181625	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2312573	0.84[EUR][1000 genomes]
rs35886191	0.96[ASN][1000 genomes]
rs3738167	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4143026	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs6656461	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs6656705	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs6659325	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6666600	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs6696973	0.86[CEU][hapmap]
rs6697365	0.86[CEU][hapmap]
rs7512401	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7524680	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs7528346	0.82[EUR][1000 genomes]
rs7537454	0.86[CEU][hapmap]
rs7541249	0.91[CEU][hapmap]
rs920987	0.86[CEU][hapmap]
rs963141	0.86[CEU][hapmap]
rs9659684	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs9660797	0.91[CEU][hapmap];0.85[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6588216	TCTEX1D1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67090400-67155000	Weak transcription	Fetal Heart	heart
2	chr1:67109600-67155000	Weak transcription	Brain Anterior Caudate	brain
3	chr1:67111400-67154800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:67114200-67156400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:67135200-67154200	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:67135600-67155400	Weak transcription	Brain Substantia Nigra	brain
7	chr1:67137400-67148000	Weak transcription	Fetal Brain Female	brain
8	chr1:67137600-67155000	Weak transcription	Brain Germinal Matrix	brain
9	chr1:67137800-67155000	Weak transcription	Fetal Brain Male	brain
10	chr1:67138000-67147200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:67138000-67154800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:67139200-67146400	Weak transcription	Fetal Lung	lung
13	chr1:67139600-67148000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:67140400-67154800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:67140600-67161200	Weak transcription	Esophagus	oesophagus
16	chr1:67140800-67147400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:67141200-67148800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:67142400-67148000	Weak transcription	Aorta	Aorta
19	chr1:67142600-67147200	Weak transcription	NHLF	lung
20	chr1:67142800-67147200	Weak transcription	NHDF-Ad	bronchial
21	chr1:67143400-67149800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:67143600-67147200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:67143600-67149600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:67144600-67147200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:67144600-67147200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:67144600-67147200	Weak transcription	HUVEC	blood vessel
27	chr1:67144600-67147200	Weak transcription	Osteobl	bone
28	chr1:67144600-67155000	Weak transcription	Left Ventricle	heart
29	chr1:67144600-67160800	Weak transcription	Lung	lung
30	chr1:67144800-67147000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:67144800-67147200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:67145000-67150200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:67145200-67146200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:67145400-67146200	Strong transcription	Brain Angular Gyrus	brain
35	chr1:67145400-67147400	Weak transcription	NH-A	brain
36	chr1:67145400-67150200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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