Variant report

Variant	rs158392
Chromosome Location	chr10:43144231-43144232
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43132537..43136859-chr10:43137751..43144882,8	MCF-7	breast:
2	chr10:43144117..43146746-chr10:43147930..43151042,3	K562	blood:

Variant related genes	Relation type
ENSG00000272373	Chromatin interaction
ENSG00000196693	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs158373	0.85[CEU][hapmap];0.96[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs158376	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158384	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158385	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158389	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158390	0.84[ASN][1000 genomes]
rs210224	0.80[CEU][hapmap]
rs210258	0.85[CEU][hapmap]
rs210261	0.81[CEU][hapmap]
rs210272	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs210278	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs210279	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs210284	0.92[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs210287	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2184238	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2473118	0.85[ASN][1000 genomes]
rs2484298	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs289182	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs289183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2982229	0.80[CEU][hapmap]
rs590937	0.86[ASN][1000 genomes]
rs668169	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs668649	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817455	chr10:42607635-43151812	Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv895064	chr10:42783481-43243325	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
9	nsv469725	chr10:42965130-43178323	Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv482513	chr10:42965130-43178323	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
12	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	esv3350301	chr10:43140755-43150235	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs158392	LINC00839	cis	Adipose Subcutaneous	GTEx
rs158392	LINC00839	cis	Esophagus Muscularis	GTEx
rs158392	LINC00839	cis	Esophagus Mucosa	GTEx
rs158392	LINC00839	cis	Artery Aorta	GTEx
rs158392	LINC00839	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43135200-43145600	Weak transcription	Primary T cells from cord blood	blood
2	chr10:43139400-43144400	Enhancers	Fetal Intestine Small	intestine
3	chr10:43141600-43145800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:43141800-43145800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:43142000-43145600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr10:43142600-43147000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:43142800-43147200	Weak transcription	Stomach Mucosa	stomach
8	chr10:43143000-43146000	Weak transcription	Fetal Intestine Large	intestine
9	chr10:43143000-43148600	Enhancers	K562	blood
10	chr10:43143400-43148200	Weak transcription	Fetal Kidney	kidney
11	chr10:43143600-43144800	Weak transcription	Pancreas	Pancrea

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