Variant report

Variant	rs1602543
Chromosome Location	chr15:40066355-40066356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1166717	0.83[ASN][1000 genomes]
rs1166721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12324408	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12439384	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12591862	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs12594027	0.91[ASN][1000 genomes]
rs12594113	0.87[ASN][1000 genomes]
rs12595664	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1491625	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16969786	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1872762	0.80[ASN][1000 genomes]
rs1906162	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1906165	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638012	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60676466	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6492913	0.87[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492915	1.00[CEU][hapmap]
rs6492916	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67248221	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67895637	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165244	1.00[CEU][hapmap]
rs7168010	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7169027	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72727074	0.87[ASN][1000 genomes]
rs72727076	0.87[ASN][1000 genomes]
rs73397128	0.85[ASN][1000 genomes]
rs8028323	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8036018	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8182052	0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40053400-40069400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:40054400-40069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:40059400-40074400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:40063200-40066600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:40063800-40066600	Weak transcription	GM12878-XiMat	blood
6	chr15:40063800-40067800	Weak transcription	Esophagus	oesophagus
7	chr15:40063800-40068800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:40063800-40068800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:40063800-40069000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:40063800-40074000	Weak transcription	Brain Angular Gyrus	brain
11	chr15:40064000-40066800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr15:40064000-40069400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40064000-40074000	Weak transcription	Brain Anterior Caudate	brain
14	chr15:40064200-40073800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:40064400-40066600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:40064400-40066600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:40064400-40067000	Weak transcription	Lung	lung
18	chr15:40064400-40069400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:40064400-40069600	Weak transcription	HSMMtube	muscle
20	chr15:40064400-40069600	Weak transcription	NH-A	brain
21	chr15:40064400-40069600	Weak transcription	NHDF-Ad	bronchial
22	chr15:40064400-40074200	Weak transcription	Osteobl	bone
23	chr15:40064600-40069400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:40064600-40069600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:40064600-40070000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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