Variant report

Variant	rs17374239
Chromosome Location	chr3:59921786-59921787
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1038516	1.00[CHB][hapmap]
rs10510820	1.00[CHB][hapmap]
rs11130741	1.00[JPT][hapmap]
rs12486471	1.00[JPT][hapmap]
rs12489929	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12490525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12490649	1.00[JPT][hapmap]
rs17061712	1.00[JPT][hapmap]
rs17253376	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap]
rs17254898	1.00[JPT][hapmap]
rs17309998	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17320834	1.00[JPT][hapmap]
rs17375293	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1872531	1.00[ASN][1000 genomes]
rs212040	1.00[CHB][hapmap]
rs2366968	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs35019677	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3772446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3772451	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772466	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3772479	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs55673050	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6786862	1.00[CHB][hapmap]
rs73104516	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73104528	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73104555	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931317	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs931321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9877140	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[ASN][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	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
3	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
4	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
5	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59914800-59928400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr3:59915600-59922600	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr3:59915800-59925400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:59916400-59927000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:59917200-59924600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:59918800-59925600	Weak transcription	Fetal Thymus	thymus
7	chr3:59919600-59925000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:59920800-59926200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:59920800-59928800	Strong transcription	Dnd41	blood
10	chr3:59921000-59925400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:59921200-59925400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:59921400-59921800	Weak transcription	Primary T cells from cord blood	blood
13	chr3:59921400-59922400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:59921400-59924600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:59921600-59925000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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