Variant report

Variant	rs209394
Chromosome Location	chr10:43142034-43142035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43137709..43140155-chr10:43140411..43142301,2	MCF-7	breast:
2	chr10:43132537..43136859-chr10:43137751..43144882,8	MCF-7	breast:
3	chr10:43141512..43143238-chr10:43157022..43158551,2	MCF-7	breast:
4	chr10:43131361..43135006-chr10:43140847..43143635,4	MCF-7	breast:
5	chr10:43137680..43139181-chr10:43140744..43142599,2	MCF-7	breast:
6	chr10:43139793..43143653-chr10:43148005..43150962,3	K562	blood:
7	chr10:43139593..43142525-chr10:43154895..43157276,2	K562	blood:

Variant related genes	Relation type
ENSG00000232109	Chromatin interaction
ENSG00000196693	Chromatin interaction
ENSG00000272373	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11239747	0.88[JPT][hapmap]
rs11239751	0.87[JPT][hapmap]
rs1147916	0.81[EUR][1000 genomes]
rs1147917	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1147918	0.80[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1147919	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11499099	0.86[JPT][hapmap]
rs11812880	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs12265862	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs12413418	0.93[JPT][hapmap]
rs12414224	0.92[JPT][hapmap]
rs1255395	0.80[CEU][hapmap];0.85[CHB][hapmap]
rs1255396	0.80[CEU][hapmap];0.85[CHB][hapmap]
rs17343443	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs1810459	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2473112	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2473115	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2473116	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2484296	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504025	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949026	0.84[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs209394	LINC00839	cis	lung	GTEx
rs209394	RP11-313J2.1	cis	Nerve Tibial	GTEx
rs209394	LINC00839	cis	Artery Tibial	GTEx
rs209394	LINC00839	cis	Artery Aorta	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43134600-43142200	Weak transcription	Aorta	Aorta
2	chr10:43134800-43143200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr10:43135200-43145600	Weak transcription	Primary T cells from cord blood	blood
4	chr10:43139400-43144400	Enhancers	Fetal Intestine Small	intestine
5	chr10:43139600-43143000	Enhancers	Fetal Intestine Large	intestine
6	chr10:43140000-43143000	Enhancers	Placenta	Placenta
7	chr10:43140000-43143600	Enhancers	Pancreas	Pancrea
8	chr10:43140200-43142600	Enhancers	Duodenum Mucosa	Duodenum
9	chr10:43140800-43143000	Flanking Active TSS	K562	blood
10	chr10:43141000-43142600	Enhancers	Esophagus	oesophagus
11	chr10:43141000-43143000	Enhancers	Placenta Amnion	Placenta Amnion
12	chr10:43141600-43142200	Enhancers	Gastric	stomach
13	chr10:43141600-43142600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:43141600-43143400	Enhancers	Fetal Kidney	kidney
15	chr10:43141600-43145800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:43141800-43142400	Flanking Active TSS	Stomach Mucosa	stomach
17	chr10:43141800-43142600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr10:43141800-43142600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:43141800-43145800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:43142000-43142600	Enhancers	NHEK	skin
21	chr10:43142000-43142800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr10:43142000-43145600	Weak transcription	Primary hematopoietic stem cells	blood

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