Variant report

Variant	rs920987
Chromosome Location	chr1:67043120-67043121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1014778	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs10889633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10889639	0.86[JPT][hapmap]
rs11208934	0.96[CEU][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs11208939	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs11208948	0.83[CEU][hapmap]
rs11208951	0.83[CEU][hapmap]
rs1160675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11811699	0.87[CEU][hapmap]
rs12031054	0.87[JPT][hapmap]
rs12128857	0.96[CEU][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs1359461	0.87[JPT][hapmap]
rs1445572	1.00[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];0.98[ASN][1000 genomes]
rs1547644	0.80[CEU][hapmap]
rs1838652	1.00[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];0.98[ASN][1000 genomes]
rs2084089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738167	0.83[CEU][hapmap]
rs4143026	0.96[CEU][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs55778510	0.80[EUR][1000 genomes]
rs6588216	0.86[CEU][hapmap]
rs6656461	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs6656705	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs6666600	0.96[CEU][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap]
rs6681263	0.80[AMR][1000 genomes]
rs6696973	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67984416	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524680	0.96[CEU][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs7525509	0.86[YRI][hapmap]
rs7537440	0.83[ASW][hapmap];0.86[YRI][hapmap]
rs7537454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547794	0.86[YRI][hapmap]
rs7547857	0.86[YRI][hapmap]
rs963141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659684	0.96[CEU][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap]
rs9660797	0.96[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][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	nsv1013351	chr1:67039730-67055937	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1003016	chr1:67043120-67067119	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs920987	TCTEX1D1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67038000-67043400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:67040200-67044200	Enhancers	Fetal Heart	heart
3	chr1:67040600-67043200	Enhancers	Fetal Lung	lung
4	chr1:67040600-67044200	Enhancers	NHLF	lung
5	chr1:67040800-67043200	Enhancers	NHEK	skin
6	chr1:67040800-67044000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:67040800-67044800	Enhancers	NHDF-Ad	bronchial
8	chr1:67041000-67043400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:67041400-67043200	Enhancers	Brain Angular Gyrus	brain
10	chr1:67041400-67043200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr1:67041400-67043600	Enhancers	Brain Hippocampus Middle	brain
12	chr1:67041400-67044200	Enhancers	NH-A	brain
13	chr1:67041400-67045600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:67041600-67043200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr1:67041600-67043600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:67041600-67043600	Enhancers	Brain Substantia Nigra	brain
17	chr1:67041600-67062400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:67042000-67044000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:67042000-67045800	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:67042000-67046200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:67042000-67046400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:67042200-67045000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:67042400-67043200	Enhancers	Brain Anterior Caudate	brain
24	chr1:67042400-67043600	Enhancers	Brain Cingulate Gyrus	brain
25	chr1:67042400-67044200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:67042600-67043400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:67042600-67043400	Weak transcription	Aorta	Aorta
28	chr1:67042600-67043600	Enhancers	Fetal Brain Male	brain
29	chr1:67042600-67044800	Enhancers	Osteobl	bone
30	chr1:67042800-67044400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:67042800-67044400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:67043000-67046600	Weak transcription	Small Intestine	intestine

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