Variant report

Variant	rs10889627
Chromosome Location	chr1:67023343-67023344
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10493409	1.00[JPT][hapmap]
rs10889626	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12136922	1.00[JPT][hapmap]
rs1536112	0.85[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs17434186	1.00[JPT][hapmap]
rs17486706	1.00[JPT][hapmap]
rs17486958	1.00[JPT][hapmap]
rs1856316	1.00[JPT][hapmap]
rs1998716	0.84[CEU][hapmap]
rs4655495	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55830106	1.00[ASN][1000 genomes]
rs56283052	1.00[ASN][1000 genomes]
rs6689755	0.85[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][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	nsv1210	chr1:67017295-67033203	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10889627	TCTEX1D1	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67000800-67029800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:67009800-67028200	Weak transcription	Brain Germinal Matrix	brain
3	chr1:67010000-67029000	Weak transcription	Fetal Kidney	kidney
4	chr1:67011000-67028000	Weak transcription	HUVEC	blood vessel
5	chr1:67011800-67029800	Weak transcription	Fetal Brain Male	brain
6	chr1:67017400-67023800	Enhancers	Fetal Heart	heart
7	chr1:67018000-67023800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:67018200-67023800	Enhancers	Brain Angular Gyrus	brain
9	chr1:67019000-67023600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:67019000-67028600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:67019800-67024000	Enhancers	NHDF-Ad	bronchial
12	chr1:67020200-67028200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:67021000-67024000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:67021200-67023400	Enhancers	Brain Substantia Nigra	brain
15	chr1:67021400-67023400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:67021400-67023800	Enhancers	Brain Hippocampus Middle	brain
17	chr1:67021400-67024000	Enhancers	Brain Cingulate Gyrus	brain
18	chr1:67021600-67023400	Enhancers	Brain Anterior Caudate	brain
19	chr1:67021800-67023400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:67022200-67023400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:67022200-67025000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:67022200-67027200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:67022400-67023600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:67022400-67023800	Enhancers	NHLF	lung
25	chr1:67022400-67024000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:67022400-67024600	Weak transcription	Aorta	Aorta
27	chr1:67022400-67027200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:67022400-67028200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:67022400-67028200	Weak transcription	Left Ventricle	heart
30	chr1:67022400-67028200	Weak transcription	NH-A	brain
31	chr1:67022400-67028400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:67022400-67028400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:67022600-67023400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:67022600-67025200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:67023000-67028400	Weak transcription	NHEK	skin
36	chr1:67023200-67023600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:67023200-67023600	Enhancers	Fetal Lung	lung
38	chr1:67023200-67027600	Weak transcription	Osteobl	bone

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