Variant report

Variant	rs657808
Chromosome Location	chr1:67209818-67209819
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	chr1:67203426..67206890-chr1:67208390..67210914,3	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10889647	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs11208944	0.91[CEU][hapmap]
rs11208945	0.91[CEU][hapmap]
rs11811067	0.90[ASN][1000 genomes]
rs12043460	0.82[AMR][1000 genomes]
rs12119578	0.89[ASN][1000 genomes]
rs12138266	0.81[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12402709	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs1280309	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1325268	0.83[CHD][hapmap]
rs1408852	0.86[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs16844	0.83[CHD][hapmap]
rs2016093	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2274987	0.92[ASN][1000 genomes]
rs2647386	0.83[AMR][1000 genomes]
rs35886191	0.83[AMR][1000 genomes]
rs3738167	0.83[CHD][hapmap]
rs473470	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs485122	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs487833	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs489300	0.86[AMR][1000 genomes]
rs500905	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs512691	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]
rs523544	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs524204	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs531386	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538659	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs553729	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55771540	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs562348	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs609906	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs609939	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs610295	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs624277	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs630410	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs650202	0.81[ASW][hapmap];0.86[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes]
rs6663604	0.95[ASN][1000 genomes]
rs6679379	0.86[ASN][1000 genomes]
rs678253	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs682896	0.83[CHD][hapmap];0.81[GIH][hapmap];0.88[AMR][1000 genomes]
rs693956	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7512401	0.83[CHD][hapmap]
rs7541249	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9988481	0.85[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs657808	TCTEX1D1	cis	lung	GTEx
rs657808	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67188600-67217400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:67192000-67217200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:67192000-67217400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:67196600-67212800	Weak transcription	Fetal Brain Female	brain
5	chr1:67197000-67217600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:67205400-67217600	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:67205600-67211600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:67205600-67217600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:67205800-67211800	Weak transcription	NHDF-Ad	bronchial
10	chr1:67205800-67217000	Weak transcription	NHLF	lung
11	chr1:67205800-67217400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:67205800-67217600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:67205800-67217800	Weak transcription	Aorta	Aorta
14	chr1:67206000-67210400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:67206000-67211000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:67206000-67215600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:67206600-67210400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:67207400-67211800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:67207400-67217400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:67207400-67217400	Weak transcription	Brain Anterior Caudate	brain
21	chr1:67208000-67212000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:67208000-67212000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:67208600-67212200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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