Variant report

Variant	rs17061678
Chromosome Location	chr3:59977537-59977538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10510821	0.89[ASN][1000 genomes]
rs12107803	0.84[AFR][1000 genomes]
rs12152244	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17031569	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17061546	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17061598	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17061683	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17061684	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17061689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17061708	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17061716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2687898	0.89[ASN][1000 genomes]
rs3772474	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3772487	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3772489	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3772503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3772504	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3821484	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57561694	0.88[AMR][1000 genomes]
rs58731594	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59871933	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60751140	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs62240114	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877030	0.89[ASN][1000 genomes]
rs72877033	0.89[ASN][1000 genomes]
rs72877036	0.89[ASN][1000 genomes]
rs7626013	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9815985	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:16 , 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	chr3:59968400-59982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:59972800-59980400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:59972800-59983600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:59973200-59977800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr3:59974200-59983000	Enhancers	Fetal Thymus	thymus
8	chr3:59974400-59983000	Enhancers	Thymus	Thymus
9	chr3:59975200-59979200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:59975200-59984000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:59975600-59978800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:59976000-59981000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:59976800-59984000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:59977000-59981600	Strong transcription	Dnd41	blood
15	chr3:59977200-59983800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr3:59977400-59977600	Enhancers	Primary T cells from cord blood	blood

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