Variant report

Variant	rs682896
Chromosome Location	chr1:67186062-67186063
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:50)

rs_ID	r²[population]
rs10789216	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10889647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10889649	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11208944	0.82[CHD][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11208945	0.82[CHD][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11208948	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11208951	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11811067	0.80[ASN][1000 genomes]
rs11811699	0.82[CHD][hapmap]
rs12043460	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12063436	0.96[ASN][1000 genomes]
rs12119578	0.81[ASN][1000 genomes]
rs12138266	0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs12402709	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1325268	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1408852	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]
rs1498354	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1547644	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16844	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2181625	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2312573	0.88[ASN][1000 genomes]
rs35886191	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3738167	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4655651	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs473470	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs485122	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs487833	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs489300	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510771	1.00[YRI][hapmap]
rs512691	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]
rs523544	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs524204	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs538659	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs553729	1.00[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs562348	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs609707	1.00[YRI][hapmap]
rs609906	0.82[AMR][1000 genomes]
rs609939	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs610295	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs624277	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs650202	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657808	0.83[CHD][hapmap];0.81[GIH][hapmap];0.88[AMR][1000 genomes]
rs6659325	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6679379	0.84[ASN][1000 genomes]
rs678253	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs678499	1.00[YRI][hapmap]
rs693956	0.89[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7512401	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7528346	0.86[ASN][1000 genomes]
rs9988481	0.93[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[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
rs682896	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67156800-67191400	Weak transcription	Fetal Brain Female	brain
2	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
3	chr1:67157200-67189600	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:67157400-67191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:67158200-67189400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:67158400-67191400	Weak transcription	Left Ventricle	heart
7	chr1:67158600-67189400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:67160400-67189400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:67165200-67191400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:67165400-67187600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:67165400-67191600	Weak transcription	Aorta	Aorta
12	chr1:67165400-67206800	Weak transcription	Fetal Brain Male	brain
13	chr1:67170200-67186800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:67171400-67189400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:67171400-67198000	Weak transcription	NHLF	lung
16	chr1:67177600-67189400	Weak transcription	Brain Anterior Caudate	brain
17	chr1:67177600-67189400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:67179600-67191400	Weak transcription	NHDF-Ad	bronchial
19	chr1:67181200-67191200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:67184400-67186400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:67184800-67199400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:67185000-67188600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:67185400-67191200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:67186000-67189800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:67186000-67190600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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