Variant report

Variant	rs11858284
Chromosome Location	chr15:59817846-59817847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GTF2A2-5	chr15:59817621-59818080	NONHSAT044173

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11071444	0.82[EUR][1000 genomes]
rs11071445	0.82[EUR][1000 genomes]
rs11071446	0.82[EUR][1000 genomes]
rs11853300	0.89[EUR][1000 genomes]
rs11853709	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11853900	0.94[ASN][1000 genomes]
rs11853953	0.94[ASN][1000 genomes]
rs11854967	0.82[EUR][1000 genomes]
rs11856047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856481	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11857239	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11857953	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs11858288	0.82[EUR][1000 genomes]
rs16941441	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs16941446	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs16941448	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs16941450	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs4597258	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[ASN][1000 genomes]
rs56327354	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57391884	0.94[ASN][1000 genomes]
rs57767828	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58087393	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58433957	0.94[ASN][1000 genomes]
rs59266497	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71119480	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73417042	0.94[ASN][1000 genomes]
rs73417089	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73418913	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028232	0.94[ASN][1000 genomes]
rs8028330	1.00[CHB][hapmap];0.86[MEX][hapmap]
rs8029395	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs8036164	0.94[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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv904279	chr15:59791666-59842927	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv984079	chr15:59816507-59823194	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59807000-59818000	Enhancers	Primary B cells from peripheral blood	blood
2	chr15:59812600-59818000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:59816000-59818000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr15:59817000-59818000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr15:59817000-59824600	Weak transcription	GM12878-XiMat	blood
6	chr15:59817200-59818000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr15:59817200-59818000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr15:59817200-59820200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:59817600-59818000	Enhancers	Fetal Brain Female	brain
10	chr15:59817600-59820600	Weak transcription	Primary B cells from cord blood	blood
11	chr15:59817800-59818000	Enhancers	Primary hematopoietic stem cells	blood

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