Variant report

Variant	rs512691
Chromosome Location	chr1:67197944-67197945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10789216	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10889647	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]
rs10889649	0.86[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs11208944	0.91[CEU][hapmap]
rs11208945	0.91[CEU][hapmap]
rs11208948	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs11208951	0.86[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs11811067	0.93[ASN][1000 genomes]
rs12043460	0.81[AMR][1000 genomes]
rs12063436	0.84[ASN][1000 genomes]
rs12119578	0.94[ASN][1000 genomes]
rs12138266	0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12402709	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs1280309	0.95[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1315210	0.82[ASN][1000 genomes]
rs1325268	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1408852	0.86[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1498354	0.86[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1547644	0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs16844	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2016093	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2181625	0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2647386	0.88[AMR][1000 genomes]
rs35886191	0.82[AMR][1000 genomes]
rs3738167	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs473470	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs485122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487833	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs489300	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs492358	0.81[AMR][1000 genomes]
rs500905	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs523544	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs524204	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs531386	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs538659	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs553729	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55771540	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs562348	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609906	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs609939	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs610295	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs624277	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs630410	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs650202	0.86[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs657808	1.00[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6659325	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs6663604	0.82[ASN][1000 genomes]
rs6679379	0.97[ASN][1000 genomes]
rs678253	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs682896	0.93[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs693956	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7512401	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7541249	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs9988481	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs512691	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	chr1:67190200-67201200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:67191800-67204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:67191800-67204800	Weak transcription	Lung	lung
10	chr1:67192000-67204600	Weak transcription	Aorta	Aorta
11	chr1:67192000-67204800	Weak transcription	Left Ventricle	heart
12	chr1:67192000-67217200	Weak transcription	Brain Angular Gyrus	brain
13	chr1:67192000-67217400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:67192200-67204600	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:67192200-67208200	Weak transcription	Brain Substantia Nigra	brain
16	chr1:67192400-67204200	Weak transcription	Brain Anterior Caudate	brain
17	chr1:67193000-67199600	Enhancers	Primary hematopoietic stem cells	blood
18	chr1:67193800-67199600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:67194200-67198000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:67194200-67198200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:67195200-67198000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:67195200-67198000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:67195400-67198200	Weak transcription	Primary T cells from cord blood	blood
24	chr1:67195400-67198400	Weak transcription	NHEK	skin
25	chr1:67195400-67198600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:67195400-67198800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:67195400-67199800	Enhancers	Dnd41	blood
28	chr1:67196600-67212800	Weak transcription	Fetal Brain Female	brain
29	chr1:67196800-67198400	Enhancers	NHDF-Ad	bronchial
30	chr1:67196800-67199800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:67197000-67201200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:67197000-67217600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:67197200-67199200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:67197200-67199600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr1:67197400-67199800	Enhancers	Osteobl	bone
36	chr1:67197600-67204600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:67197800-67198000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:67197800-67198200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:67197800-67199600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:67197800-67199600	Enhancers	HUVEC	blood vessel

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