Variant report

Variant	rs2016093
Chromosome Location	chr1:67215438-67215439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10789216	0.84[CEU][hapmap]
rs10889649	0.84[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs11208948	0.84[AMR][1000 genomes]
rs11208951	0.80[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs11811067	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11811699	0.83[CEU][hapmap]
rs12119578	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12138266	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1280309	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1325268	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs1498354	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs1547644	0.80[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs16844	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs2181625	0.83[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs2274987	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2312573	0.82[AMR][1000 genomes]
rs3738167	0.86[AMR][1000 genomes]
rs473470	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs485122	0.82[ASN][1000 genomes]
rs487833	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs500905	0.96[ASN][1000 genomes]
rs512691	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs523544	0.87[ASN][1000 genomes]
rs524204	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs531386	0.98[ASN][1000 genomes]
rs538659	0.87[ASN][1000 genomes]
rs553729	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs562348	0.85[ASN][1000 genomes]
rs609906	0.81[ASN][1000 genomes]
rs609939	0.87[ASN][1000 genomes]
rs610295	0.85[ASN][1000 genomes]
rs624277	0.88[ASN][1000 genomes]
rs630410	0.97[ASN][1000 genomes]
rs657808	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6588216	0.82[CEU][hapmap]
rs6659325	0.84[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes]
rs6663604	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679379	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs678253	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs693956	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7512401	0.83[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs7541249	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9988481	0.89[JPT][hapmap];0.82[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
rs2016093	TCTEX1D1	cis	Whole Blood	GTEx
rs2016093	TCTEX1D1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:27 , 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	chr1:67197000-67217600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:67205400-67217600	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:67205600-67217600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:67205800-67217000	Weak transcription	NHLF	lung
8	chr1:67205800-67217400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:67205800-67217600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:67205800-67217800	Weak transcription	Aorta	Aorta
11	chr1:67206000-67215600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:67207400-67217400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:67207400-67217400	Weak transcription	Brain Anterior Caudate	brain
14	chr1:67211600-67216800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:67212600-67216000	Enhancers	Osteobl	bone
16	chr1:67212800-67217600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:67213000-67217200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:67213200-67217600	Enhancers	HUVEC	blood vessel
19	chr1:67213600-67217600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:67213800-67217600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:67213800-67217600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:67214600-67217200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:67214800-67215600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:67215000-67215800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:67215200-67215800	Enhancers	NHDF-Ad	bronchial
26	chr1:67215200-67217200	Enhancers	Primary hematopoietic stem cells	blood
27	chr1:67215400-67217400	Enhancers	Primary T cells from cord blood	blood

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