Variant report

Variant	rs17375746
Chromosome Location	chr3:59957108-59957109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf67-3	chr3:59956578-59958982	NONHSAT090157

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10510826	1.00[CHB][hapmap]
rs12152244	1.00[CHB][hapmap]
rs12487051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs12495052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12495662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12497400	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs13314734	1.00[CHB][hapmap]
rs17061683	1.00[CHB][hapmap]
rs17061684	1.00[CHB][hapmap]
rs17254065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17254231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17254574	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17255191	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17319929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17320006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17394135	1.00[CHB][hapmap]
rs4411839	1.00[CHB][hapmap]
rs58526463	0.93[EUR][1000 genomes]
rs62238355	0.95[EUR][1000 genomes]
rs62238356	0.96[EUR][1000 genomes]
rs62238357	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62238368	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62240079	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62240080	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62240081	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62240082	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62240083	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62240084	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62240086	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62240087	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62240088	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62240089	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62240090	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62240091	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62240113	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62240115	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62240117	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62240119	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6767115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6797938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6798364	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6800973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs802773	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59943200-59964400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:59943800-59959600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:59946400-59958200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:59948000-59957600	Weak transcription	Dnd41	blood
5	chr3:59952000-59961600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:59952000-59964400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:59956200-59957600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:59956200-59964200	Weak transcription	Fetal Thymus	thymus
9	chr3:59956400-59960800	Strong transcription	Primary T cells from cord blood	blood

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