Variant report

Variant	rs62240117
Chromosome Location	chr3:59968238-59968239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10510826	1.00[ASN][1000 genomes]
rs12152244	1.00[ASN][1000 genomes]
rs12487051	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495052	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495662	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497400	1.00[ASN][1000 genomes]
rs13314734	1.00[ASN][1000 genomes]
rs17061683	1.00[ASN][1000 genomes]
rs17061684	1.00[ASN][1000 genomes]
rs17254065	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17254231	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17254574	1.00[ASN][1000 genomes]
rs17255191	1.00[ASN][1000 genomes]
rs17310854	1.00[ASN][1000 genomes]
rs17311592	1.00[ASN][1000 genomes]
rs17312006	1.00[ASN][1000 genomes]
rs17319929	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17320006	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17375746	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17376950	1.00[ASN][1000 genomes]
rs17377293	1.00[ASN][1000 genomes]
rs57249968	1.00[ASN][1000 genomes]
rs57561694	1.00[ASN][1000 genomes]
rs58526463	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59871933	1.00[ASN][1000 genomes]
rs60287158	1.00[ASN][1000 genomes]
rs62238355	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62238356	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62238357	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62238368	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62238369	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62238370	1.00[ASN][1000 genomes]
rs62238371	1.00[ASN][1000 genomes]
rs62240079	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240080	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240081	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240082	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240083	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240084	0.90[EUR][1000 genomes]
rs62240086	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240087	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240088	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240089	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240090	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240091	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240113	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240115	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240119	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767115	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797938	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798364	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800973	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877063	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs802773	0.93[EUR][1000 genomes];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	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:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59961600-59969000	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:59963000-59969400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:59964400-59968400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr3:59964400-59970600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:59964600-59969000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:59964600-59969600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:59964800-59968400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:59964800-59969000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:59965600-59974600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:59966000-59968400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr3:59967200-59968400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:59967200-59969400	Enhancers	Dnd41	blood
13	chr3:59967400-59968400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:59967400-59970000	Weak transcription	Fetal Thymus	thymus
15	chr3:59967400-59970200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:59967400-59971400	Weak transcription	Thymus	Thymus
17	chr3:59967400-59974400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr3:59967400-59993000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:59967800-59968400	Genic enhancers	Primary T cells from cord blood	blood
20	chr3:59968000-59986600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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