Variant report

Variant	rs6543598
Chromosome Location	chr2:31295230-31295231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10166079	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10175305	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10188244	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs10189705	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10196495	0.83[EUR][1000 genomes]
rs10205657	0.90[EUR][1000 genomes]
rs1075688	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1075689	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11124239	0.85[EUR][1000 genomes]
rs11124240	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11674713	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11686425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11692265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11888670	0.83[EUR][1000 genomes]
rs12712310	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs12712311	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs12996218	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13003016	0.85[EUR][1000 genomes]
rs13029054	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs1862975	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs1862977	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1862978	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1862979	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1862981	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1991103	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1991104	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2098787	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2161832	0.92[EUR][1000 genomes]
rs2161833	0.92[EUR][1000 genomes]
rs2194467	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2194468	0.95[EUR][1000 genomes]
rs2194469	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2365192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2365196	0.85[EUR][1000 genomes]
rs2365197	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2365199	0.87[EUR][1000 genomes]
rs2365200	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2365201	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2365205	0.91[EUR][1000 genomes]
rs2365206	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs35285211	0.87[EUR][1000 genomes]
rs4951965	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6543599	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6543600	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6709814	0.95[EUR][1000 genomes]
rs6713789	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6718085	0.85[EUR][1000 genomes]
rs6718097	0.85[EUR][1000 genomes]
rs6722828	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6729079	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6732067	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6743541	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs6753457	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6760532	0.94[EUR][1000 genomes]
rs6760971	0.94[EUR][1000 genomes]
rs7565689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570822	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7583033	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7583218	0.92[EUR][1000 genomes]
rs7586148	0.89[CEU][hapmap]
rs7600547	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9973425	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3352229	chr2:31295039-31295296	Weak transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31278200-31310800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:31278800-31306800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr2:31284000-31301800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:31287200-31297000	Weak transcription	Aorta	Aorta
5	chr2:31288800-31305000	Weak transcription	Right Atrium	heart
6	chr2:31288800-31308400	Weak transcription	Spleen	Spleen
7	chr2:31291000-31298400	Weak transcription	Brain Germinal Matrix	brain
8	chr2:31293000-31298000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:31293800-31298200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:31294000-31301600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:31294200-31298400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:31294400-31298400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:31294400-31298400	Weak transcription	HMEC	breast
14	chr2:31294400-31301400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:31294600-31296600	Weak transcription	Esophagus	oesophagus
16	chr2:31294600-31297800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:31294600-31298200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:31294600-31298400	Weak transcription	NHEK	skin
19	chr2:31294600-31298600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:31294800-31297800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:31294800-31297800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:31295200-31296800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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