Variant report

Variant	rs2181625
Chromosome Location	chr1:67192271-67192272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67166132..67168879-chr1:67189803..67192452,2	K562	blood:
2	chr1:67072874..67073739-chr1:67191676..67192371,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1014778	0.84[CEU][hapmap]
rs10789216	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10889647	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10889649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208934	0.83[CEU][hapmap]
rs11208939	0.84[CEU][hapmap]
rs11208948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11208951	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1160675	0.80[CEU][hapmap]
rs11811067	0.82[ASN][1000 genomes]
rs11811699	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12063436	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12119578	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12128857	0.83[CEU][hapmap]
rs12138266	0.87[CEU][hapmap];0.85[CHB][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1325268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1408852	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1445572	0.80[CEU][hapmap]
rs1498354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2016093	0.83[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs2274987	0.86[AMR][1000 genomes]
rs2312573	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3738167	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143026	0.83[CEU][hapmap]
rs473470	0.80[ASN][1000 genomes]
rs485122	0.85[ASN][1000 genomes]
rs487833	0.81[ASN][1000 genomes]
rs489300	0.98[ASN][1000 genomes]
rs512691	0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs524204	0.80[ASN][1000 genomes]
rs538659	0.81[ASN][1000 genomes]
rs553729	0.80[ASN][1000 genomes]
rs562348	0.83[ASN][1000 genomes]
rs609939	0.81[ASN][1000 genomes]
rs624277	0.80[ASN][1000 genomes]
rs650202	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6588216	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6656461	0.84[CEU][hapmap]
rs6656705	0.84[CEU][hapmap]
rs6659325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6663604	0.87[AMR][1000 genomes]
rs6666600	0.83[CEU][hapmap]
rs6679379	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs682896	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs693956	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs7512401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524680	0.83[CEU][hapmap]
rs7528346	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541249	0.83[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs9659684	0.83[CEU][hapmap]
rs9660797	0.84[CEU][hapmap]
rs9988481	0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv830093	chr1:67173594-67348264	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv997677	chr1:67186675-67194280	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2181625	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
2	chr1:67165400-67206800	Weak transcription	Fetal Brain Male	brain
3	chr1:67171400-67198000	Weak transcription	NHLF	lung
4	chr1:67184800-67199400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:67186400-67205000	Weak transcription	Fetal Heart	heart
6	chr1:67188600-67217400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:67190000-67193800	Weak transcription	NH-A	brain
8	chr1:67190200-67201200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:67190600-67193600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:67190600-67195000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:67191200-67192400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:67191200-67192800	Enhancers	Primary hematopoietic stem cells	blood
13	chr1:67191200-67193400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:67191400-67192600	Enhancers	Dnd41	blood
15	chr1:67191400-67192600	Enhancers	NHDF-Ad	bronchial
16	chr1:67191400-67193200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:67191400-67195000	Enhancers	HUVEC	blood vessel
18	chr1:67191600-67195400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr1:67191800-67193200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:67191800-67196200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:67191800-67204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:67191800-67204800	Weak transcription	Lung	lung
23	chr1:67192000-67193000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:67192000-67194600	Weak transcription	Primary T cells from cord blood	blood
25	chr1:67192000-67194800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:67192000-67194800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:67192000-67195800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:67192000-67195800	Weak transcription	Fetal Brain Female	brain
29	chr1:67192000-67196200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:67192000-67197800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:67192000-67204600	Weak transcription	Aorta	Aorta
32	chr1:67192000-67204800	Weak transcription	Left Ventricle	heart
33	chr1:67192000-67217200	Weak transcription	Brain Angular Gyrus	brain
34	chr1:67192000-67217400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:67192200-67192400	Enhancers	Brain Anterior Caudate	brain
36	chr1:67192200-67193400	Weak transcription	Osteobl	bone
37	chr1:67192200-67193800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:67192200-67194400	Weak transcription	Thymus	Thymus
39	chr1:67192200-67204600	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:67192200-67208200	Weak transcription	Brain Substantia Nigra	brain

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