Variant report

Variant	rs2687899
Chromosome Location	chr3:59970958-59970959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10490808	0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11130742	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130743	0.94[ASN][1000 genomes]
rs12630463	0.88[ASN][1000 genomes]
rs13061330	1.00[ASN][1000 genomes]
rs13063413	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs13070349	0.94[ASN][1000 genomes]
rs13070475	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13077692	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs13092173	0.85[ASN][1000 genomes]
rs13092997	0.88[ASN][1000 genomes]
rs13094437	0.88[ASN][1000 genomes]
rs2736794	0.89[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs3772464	0.81[CHD][hapmap]
rs3772468	0.88[ASN][1000 genomes]
rs3772473	0.87[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs3772483	0.87[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs3772484	0.88[ASN][1000 genomes]
rs3772491	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3772492	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3772505	0.81[JPT][hapmap]
rs3821478	0.86[ASN][1000 genomes]
rs3821479	0.87[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs3821480	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821481	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3821482	0.95[ASN][1000 genomes]
rs6771484	0.88[ASN][1000 genomes]
rs6771698	0.88[ASN][1000 genomes]
rs6805337	0.87[ASN][1000 genomes]
rs7640107	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs802772	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs802774	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs802775	0.89[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs812445	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv876838	chr3:59952152-59999690	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590388	chr3:59957252-60018326	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv965380	chr3:59970574-59976399	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59965600-59974600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr3:59967400-59971400	Weak transcription	Thymus	Thymus
3	chr3:59967400-59974400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr3:59967400-59993000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:59968000-59986600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:59968400-59971400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:59968400-59971800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:59968400-59982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:59969000-59971600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:59969000-59971600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:59969400-59971600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:59970000-59971600	ZNF genes & repeats	Fetal Thymus	thymus
13	chr3:59970000-59971800	Genic enhancers	Primary T cells from cord blood	blood
14	chr3:59970000-59972000	ZNF genes & repeats	Dnd41	blood
15	chr3:59970200-59971000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr3:59970400-59971200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:59970600-59971000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:59970600-59971600	Enhancers	Primary hematopoietic stem cells	blood
19	chr3:59970600-59972000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:59970800-59971000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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