Variant report

Variant	rs17254765
Chromosome Location	chr3:59986297-59986298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10510822	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs10510823	1.00[CEU][hapmap];0.87[ASN][1000 genomes]
rs11707269	0.83[CHD][hapmap]
rs1385812	0.83[CHD][hapmap]
rs1485904	0.83[CHD][hapmap]
rs17061544	1.00[CEU][hapmap];0.87[ASN][1000 genomes]
rs17061705	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs17061746	1.00[CEU][hapmap]
rs17302746	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs17302837	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap]
rs1970842	0.86[ASN][1000 genomes]
rs2101339	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs2630186	1.00[CEU][hapmap];0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs2630190	0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs3772467	1.00[CEU][hapmap];0.87[ASN][1000 genomes]
rs3772485	0.87[ASN][1000 genomes]
rs3772506	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3772507	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3772508	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3821485	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4679624	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs55659096	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55832883	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55910136	0.86[ASN][1000 genomes]
rs56257507	0.86[ASN][1000 genomes]
rs57347814	0.86[ASN][1000 genomes]
rs6802153	0.83[CHD][hapmap]
rs802771	1.00[CEU][hapmap];0.84[ASN][1000 genomes]
rs809097	0.94[CHD][hapmap]
rs9862003	0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs9879175	1.00[CEU][hapmap]

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	nsv590389	chr3:59981525-59998389	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59967400-59993000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:59968000-59986600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:59980600-59992800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr3:59983000-59986600	Weak transcription	Thymus	Thymus
5	chr3:59983000-59993200	Weak transcription	Dnd41	blood
6	chr3:59983400-59987200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:59984600-59986400	Weak transcription	Primary T cells from cord blood	blood
8	chr3:59985000-59988600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:59985600-59989200	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:59985800-59988600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:59985800-59993000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:59986000-59987600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr3:59986200-59987000	Enhancers	Fetal Thymus	thymus
14	chr3:59986200-59988200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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