Variant report

Variant	rs8026679
Chromosome Location	chr15:93466615-93466616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:93466440-93466818	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:93465510-93467462	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr15:93463583-93466834	K562	blood:	n/a	n/a
4	POLR2A	chr15:93465936-93466677	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr15:93463568-93466760	U87	brain:	n/a	n/a
6	POLR2A	chr15:93466446-93466671	GM12891	blood:	n/a	n/a
7	POLR2A	chr15:93463008-93472730	K562	blood:	n/a	n/a
8	POLR2A	chr15:93466535-93466918	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:93465500-93467122	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:93463684-93466928	GM12891	blood:	n/a	n/a
11	POLR2A	chr15:93464040-93466615	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:93466090-93466925	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
2	chr15:93350620..93356582-chr15:93455419..93466792,23	MCF-7	breast:
3	chr15:93463483..93466768-chr15:93471204..93475396,3	MCF-7	breast:

No data

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

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10520718	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1074512	0.81[EUR][1000 genomes]
rs11074120	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11857466	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11857669	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12591124	0.81[EUR][1000 genomes]
rs12592920	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12594474	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12908494	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12914956	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17610487	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1881834	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1881835	0.82[AMR][1000 genomes]
rs2388055	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34448107	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3743469	0.86[AMR][1000 genomes]
rs3784785	0.81[AMR][1000 genomes]
rs3826036	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62023146	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6497010	0.85[AMR][1000 genomes]
rs6497011	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6497013	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7174043	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7176652	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7179863	0.80[EUR][1000 genomes]
rs8024528	0.89[AMR][1000 genomes]
rs8042395	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8042632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302362	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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
rs8026679	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	chr15:93461200-93467200	Enhancers	Stomach Mucosa	stomach
3	chr15:93461200-93467400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr15:93461200-93467600	Weak transcription	Fetal Brain Male	brain
5	chr15:93461200-93467600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr15:93461200-93471600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:93461600-93467600	Enhancers	Brain Cingulate Gyrus	brain
8	chr15:93461600-93471600	Weak transcription	Ovary	ovary
9	chr15:93461600-93486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:93462000-93474800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:93463200-93468000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:93463200-93486800	Strong transcription	Dnd41	blood
14	chr15:93463400-93467600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr15:93463600-93466800	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr15:93463600-93467800	Enhancers	Small Intestine	intestine
17	chr15:93463600-93470200	Genic enhancers	Fetal Intestine Large	intestine
18	chr15:93464200-93467800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:93464200-93475000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:93464400-93469600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
21	chr15:93464400-93473600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:93464600-93467600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr15:93464600-93468000	Enhancers	Colon Smooth Muscle	Colon
24	chr15:93464800-93468400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:93464800-93469200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
26	chr15:93464800-93469600	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr15:93465000-93467400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr15:93465000-93467800	Genic enhancers	Primary T cells from cord blood	blood
29	chr15:93465000-93467800	Weak transcription	Fetal Kidney	kidney
30	chr15:93465000-93468600	Genic enhancers	A549	lung
31	chr15:93465000-93471400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:93465200-93466800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:93465200-93467200	Weak transcription	NHLF	lung
34	chr15:93465200-93467600	Weak transcription	Brain Germinal Matrix	brain
35	chr15:93465200-93467600	Weak transcription	Lung	lung
36	chr15:93465200-93468200	Weak transcription	Fetal Brain Female	brain
37	chr15:93465400-93467400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:93465400-93468600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:93465400-93469600	Strong transcription	Fetal Stomach	stomach
40	chr15:93465400-93488400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:93465600-93466800	Genic enhancers	Rectal Mucosa Donor 31	rectum
42	chr15:93465600-93468800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:93465600-93469000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:93465600-93469600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:93465600-93472000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr15:93465800-93467000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr15:93465800-93467200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:93465800-93467600	Weak transcription	Esophagus	oesophagus
49	chr15:93465800-93467600	Weak transcription	Gastric	stomach
50	chr15:93465800-93467800	Genic enhancers	Brain Anterior Caudate	brain

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