Variant report

Variant	rs10889647
Chromosome Location	chr1:67154496-67154497
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10789216	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10889649	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11208944	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11208945	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11208948	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11208949	1.00[YRI][hapmap]
rs11208951	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12029896	1.00[YRI][hapmap]
rs12043460	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12063436	0.97[ASN][1000 genomes]
rs12138266	0.80[ASN][1000 genomes]
rs12402709	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1325268	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1408852	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498354	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1547644	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16844	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2181625	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2312573	0.86[ASN][1000 genomes]
rs35886191	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3738167	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4655651	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs473470	0.81[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes]
rs485122	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs487833	0.82[CEU][hapmap];0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs489300	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs512691	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs523544	0.83[AMR][1000 genomes]
rs524204	0.82[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes]
rs538659	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs553729	0.85[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes]
rs562348	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs566057	0.80[YRI][hapmap]
rs609939	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs610295	0.83[AMR][1000 genomes]
rs624277	0.81[AMR][1000 genomes]
rs650202	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs657808	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs6659325	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6679379	0.82[ASN][1000 genomes]
rs678253	0.82[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes]
rs682896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs693956	0.81[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs7512401	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7528346	0.89[ASN][1000 genomes]
rs9988481	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10889647	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:34 , 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	chr1:67135600-67155400	Weak transcription	Brain Substantia Nigra	brain
6	chr1:67137600-67155000	Weak transcription	Brain Germinal Matrix	brain
7	chr1:67137800-67155000	Weak transcription	Fetal Brain Male	brain
8	chr1:67138000-67154800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:67140400-67154800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:67140600-67161200	Weak transcription	Esophagus	oesophagus
11	chr1:67144600-67155000	Weak transcription	Left Ventricle	heart
12	chr1:67144600-67160800	Weak transcription	Lung	lung
13	chr1:67146200-67154800	Weak transcription	Brain Angular Gyrus	brain
14	chr1:67148200-67156600	Weak transcription	Aorta	Aorta
15	chr1:67148400-67154600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:67148400-67154800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:67148400-67155000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:67148800-67154800	Weak transcription	NHLF	lung
19	chr1:67149000-67154800	Weak transcription	Fetal Brain Female	brain
20	chr1:67149200-67161000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:67151800-67154800	Weak transcription	NHDF-Ad	bronchial
22	chr1:67152000-67154800	Weak transcription	NH-A	brain
23	chr1:67152000-67155000	Weak transcription	Osteobl	bone
24	chr1:67152000-67155200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:67152000-67162800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:67152600-67155800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:67152800-67159800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:67153400-67161200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:67153600-67154800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:67153600-67155600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:67153600-67155800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:67154000-67155400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:67154200-67157200	Strong transcription	Brain Hippocampus Middle	brain
34	chr1:67154400-67156200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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