Variant report

Variant	rs1408852
Chromosome Location	chr1:67155328-67155329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10789216	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10889647	0.95[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];1.00[ASN][1000 genomes]
rs10889649	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11208944	0.95[CEU][hapmap];0.81[CHD][hapmap];0.80[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11208945	0.95[CEU][hapmap];0.81[CHD][hapmap];0.80[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11208948	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11208949	1.00[YRI][hapmap]
rs11208951	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11811699	0.81[CHD][hapmap]
rs12029896	1.00[YRI][hapmap]
rs12031054	0.81[CEU][hapmap]
rs12043460	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12063436	0.97[ASN][1000 genomes]
rs12138266	0.86[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12402709	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1280309	0.82[CEU][hapmap]
rs1325268	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1359461	0.81[CEU][hapmap]
rs1498354	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1547644	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16844	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2181625	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2312573	0.86[ASN][1000 genomes]
rs2454325	0.80[YRI][hapmap]
rs35886191	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3738167	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4655651	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs473470	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs485122	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs487833	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs489300	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs512691	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]
rs523544	0.83[AMR][1000 genomes]
rs524204	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs538659	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs553729	0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes]
rs562348	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs566057	0.80[YRI][hapmap]
rs609939	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs610295	0.83[AMR][1000 genomes]
rs624277	0.81[AMR][1000 genomes]
rs650202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs657808	0.86[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs6659325	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6679379	0.82[ASN][1000 genomes]
rs678253	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs682896	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs693956	0.86[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs7512401	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7528346	0.89[ASN][1000 genomes]
rs9988481	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[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
rs1408852	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67114200-67156400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:67135600-67155400	Weak transcription	Brain Substantia Nigra	brain
3	chr1:67140600-67161200	Weak transcription	Esophagus	oesophagus
4	chr1:67144600-67160800	Weak transcription	Lung	lung
5	chr1:67148200-67156600	Weak transcription	Aorta	Aorta
6	chr1:67149200-67161000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:67152000-67162800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:67152600-67155800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:67152800-67159800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:67153400-67161200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:67153600-67155600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:67153600-67155800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:67154000-67155400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:67154200-67157200	Strong transcription	Brain Hippocampus Middle	brain
15	chr1:67154400-67156200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:67154600-67156200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:67154800-67155400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:67154800-67155600	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:67154800-67155600	Strong transcription	NHDF-Ad	bronchial
20	chr1:67154800-67155800	Strong transcription	Brain Angular Gyrus	brain
21	chr1:67154800-67155800	Strong transcription	NH-A	brain
22	chr1:67154800-67156000	Strong transcription	NHLF	lung
23	chr1:67154800-67156200	Strong transcription	Brain Cingulate Gyrus	brain
24	chr1:67154800-67156800	Strong transcription	Fetal Brain Female	brain
25	chr1:67154800-67157200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:67154800-67157400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:67155000-67155600	Strong transcription	Osteobl	bone
28	chr1:67155000-67155800	Strong transcription	Brain Anterior Caudate	brain
29	chr1:67155000-67155800	Strong transcription	Fetal Brain Male	brain
30	chr1:67155000-67155800	Strong transcription	Fetal Heart	heart
31	chr1:67155000-67156000	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr1:67155000-67156000	Strong transcription	Left Ventricle	heart
33	chr1:67155000-67157000	Strong transcription	Brain Germinal Matrix	brain
34	chr1:67155200-67158200	Strong transcription	Muscle Satellite Cultured Cells	--

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