Variant report

Variant	rs687342
Chromosome Location	chr3:59853580-59853581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1485725	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1485726	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1485729	0.87[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1485733	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17493	0.95[GIH][hapmap]
rs2629896	0.87[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2687903	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3112498	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4679614	0.95[GIH][hapmap]
rs615964	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs621666	0.85[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs669229	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs670885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs677703	0.87[CEU][hapmap];0.99[EUR][1000 genomes]
rs678981	0.87[CEU][hapmap];0.99[EUR][1000 genomes]
rs684753	0.95[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv460564	chr3:59821071-59927727	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv590384	chr3:59821071-59927727	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv460565	chr3:59842644-59877988	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv470616	chr3:59842644-59877988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv590385	chr3:59842644-59877988	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv590386	chr3:59846067-59912377	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59843600-59854200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:59850000-59864000	Weak transcription	Fetal Thymus	thymus
3	chr3:59851600-59857800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:59852200-59855200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:59852400-59854400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:59852400-59857400	Weak transcription	Dnd41	blood
7	chr3:59852600-59855200	Enhancers	Primary T cells from cord blood	blood
8	chr3:59852800-59855000	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:59852800-59859800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:59853200-59853800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:59853200-59855000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr3:59853400-59853800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:59853400-59853800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:59853400-59854000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:59853400-59855200	Enhancers	Primary T helper cells fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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