Variant report

Variant	rs10520716
Chromosome Location	chr15:93491017-93491018
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:93490809-93491038	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:93490561-93491103	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:93490825-93491024	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:93490854-93491105	GM12892	blood:	n/a	n/a
5	POLR2A	chr15:93490516-93491052	GM12891	blood:	n/a	n/a
6	POLR2A	chr15:93490462-93491070	K562	blood:	n/a	n/a
7	POLR2A	chr15:93490849-93491038	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:93490299-93491021	U87	brain:	n/a	n/a
9	POLR2A	chr15:93490893-93491046	HepG2	liver:	n/a	n/a
10	POLR2A	chr15:93490114-93491661	K562	blood:	n/a	n/a
11	POLR2A	chr15:93490305-93491021	U87	brain:	n/a	n/a
12	POLR2A	chr15:93490314-93491086	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr15:93490760-93491105	K562	blood:	n/a	n/a
14	POLR2A	chr15:93490319-93491180	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:93490784-93491231	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:93490841-93491052	K562	blood:	n/a	n/a
17	POLR2A	chr15:93490153-93491661	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:93481880..93488025-chr15:93488179..93492236,5	K562	blood:
2	chr15:93479767..93482269-chr15:93490198..93491804,2	K562	blood:
3	chr15:93482816..93485781-chr15:93488823..93491729,2	K562	blood:

No data

Variant related genes	Relation type
CHD2	TF binding region
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10520719	0.86[JPT][hapmap]
rs11074120	0.81[JPT][hapmap]
rs11630582	0.86[JPT][hapmap]
rs11634207	0.86[JPT][hapmap]
rs11634566	0.89[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs12437674	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12438635	0.89[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs12443243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12594991	0.92[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs12901950	0.92[JPT][hapmap]
rs12904680	0.92[JPT][hapmap]
rs12905312	0.84[EUR][1000 genomes]
rs12906132	0.86[JPT][hapmap]
rs12907579	0.86[JPT][hapmap]
rs12908494	0.88[EUR][1000 genomes]
rs12916015	0.92[JPT][hapmap]
rs1318689	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1320819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1406714	0.92[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1534779	0.86[JPT][hapmap]
rs17525800	0.86[JPT][hapmap]
rs1881835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033844	0.86[JPT][hapmap]
rs2272457	0.86[JPT][hapmap]
rs35865218	0.92[ASN][1000 genomes]
rs3743469	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3784786	0.86[JPT][hapmap]
rs3817597	0.81[JPT][hapmap]
rs3826035	0.89[CEU][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs3826036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs4327000	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4778052	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4778065	0.85[JPT][hapmap]
rs6497009	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6497010	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7164668	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167194	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7168780	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7171151	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7175134	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7176652	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs8024528	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs8026695	0.92[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs8035739	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8042395	0.81[JPT][hapmap]
rs8042632	0.81[JPT][hapmap]
rs920389	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs961233	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
3	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
4	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10520716	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93474000-93491400	Strong transcription	Fetal Muscle Trunk	muscle
2	chr15:93474400-93492200	Strong transcription	Fetal Kidney	kidney
3	chr15:93474800-93492200	Strong transcription	HSMMtube	muscle
4	chr15:93474800-93492200	Strong transcription	Osteobl	bone
5	chr15:93474800-93501800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:93475000-93492600	Strong transcription	NHDF-Ad	bronchial
7	chr15:93475800-93492200	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr15:93476800-93492200	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:93477200-93493000	Strong transcription	Placenta	Placenta
10	chr15:93477200-93501200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr15:93478200-93491200	Strong transcription	HUVEC	blood vessel
12	chr15:93478600-93503200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:93480400-93493000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:93480600-93492200	Strong transcription	Stomach Smooth Muscle	stomach
15	chr15:93480800-93492000	Strong transcription	Colonic Mucosa	Colon
16	chr15:93480800-93492600	Strong transcription	Brain Anterior Caudate	brain
17	chr15:93480800-93494000	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:93481000-93491200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:93481000-93492800	Strong transcription	Brain Cingulate Gyrus	brain
20	chr15:93482000-93491800	Strong transcription	Fetal Intestine Large	intestine
21	chr15:93482400-93492200	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr15:93484400-93491400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:93484600-93492600	Strong transcription	Rectal Smooth Muscle	rectum
24	chr15:93485000-93492200	Strong transcription	Fetal Brain Female	brain
25	chr15:93485000-93492600	Strong transcription	Brain Hippocampus Middle	brain
26	chr15:93485000-93492600	Strong transcription	Brain Substantia Nigra	brain
27	chr15:93485000-93494600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:93485200-93492000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:93486000-93495000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:93486400-93493800	Strong transcription	Fetal Brain Male	brain
31	chr15:93486800-93493200	ZNF genes & repeats	Dnd41	blood
32	chr15:93486800-93494400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:93487600-93492000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:93487600-93494000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:93487600-93500000	Strong transcription	Brain Angular Gyrus	brain
36	chr15:93487800-93492000	Strong transcription	Psoas Muscle	Psoas
37	chr15:93488000-93492000	Strong transcription	Left Ventricle	heart
38	chr15:93488200-93493000	Strong transcription	Lung	lung
39	chr15:93488200-93493200	Strong transcription	Pancreas	Pancrea
40	chr15:93488200-93493600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
41	chr15:93488200-93494000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr15:93488200-93494000	ZNF genes & repeats	Thymus	Thymus
43	chr15:93488200-93494000	ZNF genes & repeats	GM12878-XiMat	blood
44	chr15:93488200-93494200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:93488200-93494200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:93488400-93493800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
47	chr15:93489000-93491200	Strong transcription	Stomach Mucosa	stomach
48	chr15:93489000-93494000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
49	chr15:93489200-93492600	Strong transcription	Right Ventricle	heart
50	chr15:93489200-93493400	ZNF genes & repeats	Primary B cells from cord blood	blood

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