Variant report

Variant	rs3826036
Chromosome Location	chr15:93467391-93467392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:93465510-93467462	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr15:93467072-93467472	K562	blood:	n/a	n/a
3	POLR2A	chr15:93463008-93472730	K562	blood:	n/a	n/a
4	POLR2A	chr15:93466919-93467828	U87	brain:	n/a	n/a
5	POLR2A	chr15:93467165-93467414	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr15:93467211-93467430	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:93467234-93467918	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
2	chr15:93352951..93354833-chr15:93466989..93469853,2	MCF-7	breast:

Variant related genes	Relation type
CHD2	TF binding region
ENSG00000185442	Chromatin interaction
ENSG00000258922	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10520716	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]
rs1074512	0.88[MEX][hapmap]
rs11074120	0.87[JPT][hapmap];0.86[AMR][1000 genomes]
rs11634566	0.89[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs12437674	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12438635	0.89[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs12443243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12591124	0.88[MEX][hapmap]
rs12594991	0.92[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs12901950	0.86[JPT][hapmap]
rs12904680	0.86[JPT][hapmap]
rs12908494	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916015	0.86[JPT][hapmap]
rs1318689	0.92[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1320819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs1406714	0.92[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1881834	0.83[AMR][1000 genomes]
rs1881835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28573213	0.91[ASN][1000 genomes]
rs3743469	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3826035	0.89[CEU][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs4327000	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs4778052	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6497009	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6497010	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6497013	0.92[MEX][hapmap]
rs7164668	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7167194	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs7168780	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7171151	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7173103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175134	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176652	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs8024528	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8026679	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8026695	0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs8035739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8042395	0.84[ASW][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.81[AMR][1000 genomes]
rs8042632	0.87[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs920389	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs9302362	0.91[ASW][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs961233	0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	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
8	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
rs3826036	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93457000-93489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:93461200-93467400	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr15:93461200-93467600	Weak transcription	Fetal Brain Male	brain
4	chr15:93461200-93467600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr15:93461200-93471600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:93461600-93467600	Enhancers	Brain Cingulate Gyrus	brain
7	chr15:93461600-93471600	Weak transcription	Ovary	ovary
8	chr15:93461600-93486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:93462000-93474800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:93463200-93468000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:93463200-93486800	Strong transcription	Dnd41	blood
13	chr15:93463400-93467600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr15:93463600-93467800	Enhancers	Small Intestine	intestine
15	chr15:93463600-93470200	Genic enhancers	Fetal Intestine Large	intestine
16	chr15:93464200-93467800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:93464200-93475000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:93464400-93469600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr15:93464400-93473600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr15:93464600-93467600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr15:93464600-93468000	Enhancers	Colon Smooth Muscle	Colon
22	chr15:93464800-93468400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:93464800-93469200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
24	chr15:93464800-93469600	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr15:93465000-93467400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr15:93465000-93467800	Genic enhancers	Primary T cells from cord blood	blood
27	chr15:93465000-93467800	Weak transcription	Fetal Kidney	kidney
28	chr15:93465000-93468600	Genic enhancers	A549	lung
29	chr15:93465000-93471400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:93465200-93467600	Weak transcription	Brain Germinal Matrix	brain
31	chr15:93465200-93467600	Weak transcription	Lung	lung
32	chr15:93465200-93468200	Weak transcription	Fetal Brain Female	brain
33	chr15:93465400-93467400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr15:93465400-93468600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:93465400-93469600	Strong transcription	Fetal Stomach	stomach
36	chr15:93465400-93488400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:93465600-93468800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:93465600-93469000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:93465600-93469600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:93465600-93472000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr15:93465800-93467600	Weak transcription	Esophagus	oesophagus
42	chr15:93465800-93467600	Weak transcription	Gastric	stomach
43	chr15:93465800-93467800	Genic enhancers	Brain Anterior Caudate	brain
44	chr15:93465800-93468200	Genic enhancers	Left Ventricle	heart
45	chr15:93465800-93468600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:93465800-93469200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr15:93465800-93471600	Weak transcription	Aorta	Aorta
48	chr15:93466000-93467400	Genic enhancers	Primary B cells from cord blood	blood
49	chr15:93466000-93467600	Weak transcription	Pancreas	Pancrea
50	chr15:93466000-93467800	Weak transcription	Placenta Amnion	Placenta Amnion

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