Variant report

Variant	rs10889639
Chromosome Location	chr1:67110169-67110170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1014778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10889633	0.86[JPT][hapmap]
rs11208934	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11208939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11208944	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap]
rs11208945	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap]
rs1160675	0.87[JPT][hapmap]
rs11811699	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs12031054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128857	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12402709	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs12760606	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1359461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445572	0.87[JPT][hapmap]
rs1838652	0.87[JPT][hapmap]
rs4143026	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55778510	0.99[ASN][1000 genomes]
rs6588216	0.84[JPT][hapmap]
rs6656461	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6656705	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6656752	1.00[ASN][1000 genomes]
rs6666600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6681164	0.93[ASN][1000 genomes]
rs6681263	0.97[ASN][1000 genomes]
rs6696973	0.86[JPT][hapmap]
rs6697365	0.86[JPT][hapmap]
rs7524680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7537454	0.86[JPT][hapmap]
rs920987	0.86[JPT][hapmap]
rs963141	0.86[JPT][hapmap]
rs9659684	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9660797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9662956	1.00[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
rs10889639	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67088400-67114200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:67090400-67155000	Weak transcription	Fetal Heart	heart
3	chr1:67091200-67128000	Weak transcription	NH-A	brain
4	chr1:67092000-67117200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:67092200-67114200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:67099400-67115600	Weak transcription	Fetal Lung	lung
7	chr1:67100000-67144400	Weak transcription	Left Ventricle	heart
8	chr1:67101200-67113600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:67101400-67110200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:67101600-67110800	Weak transcription	Aorta	Aorta
11	chr1:67102800-67120200	Weak transcription	Brain Germinal Matrix	brain
12	chr1:67103200-67112200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:67106200-67143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:67106800-67115800	Weak transcription	Fetal Brain Male	brain
15	chr1:67107200-67112800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:67107200-67114200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:67108000-67136200	Weak transcription	Fetal Brain Female	brain
18	chr1:67108200-67110200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:67108400-67110800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:67108600-67110400	Enhancers	Brain Hippocampus Middle	brain
21	chr1:67108600-67110800	Enhancers	Brain Substantia Nigra	brain
22	chr1:67108600-67111000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr1:67109000-67110800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:67109000-67117800	Weak transcription	Osteobl	bone
25	chr1:67109200-67110400	Weak transcription	NHDF-Ad	bronchial
26	chr1:67109200-67110800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:67109200-67120200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:67109200-67141800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:67109400-67110400	Weak transcription	Brain Angular Gyrus	brain
30	chr1:67109600-67113600	Weak transcription	NHLF	lung
31	chr1:67109600-67134200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:67109600-67155000	Weak transcription	Brain Anterior Caudate	brain
33	chr1:67110000-67110400	Enhancers	Cortex derived primary cultured neurospheres	brain

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