Variant report

Variant	rs6446102
Chromosome Location	chr3:59957116-59957117
allele	A/G
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: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11711589	0.81[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs11921436	0.88[ASN][1000 genomes]
rs13064036	0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13072228	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13075410	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1879996	0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs212034	0.93[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2630189	0.89[ASN][1000 genomes]
rs2630191	0.81[ASN][1000 genomes]
rs2736794	0.91[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2736796	0.90[ASN][1000 genomes]
rs2736802	0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs3772475	0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs3772476	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3772477	0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs3772480	0.97[ASN][1000 genomes]
rs3772482	0.86[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs3772484	0.86[JPT][hapmap]
rs6446100	0.93[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6446101	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6446103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626003	0.82[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs802775	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs809098	0.81[CEU][hapmap]
rs9819930	0.80[CHD][hapmap]
rs9865672	0.93[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs9880771	0.87[ASN][1000 genomes]
rs9881070	0.81[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][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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