Variant report

Variant	rs11070883
Chromosome Location	chr15:52483565-52483566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:52483560-52483710	A549	lung:	n/a	n/a
2	RCOR1	chr15:52483485-52483727	K562	blood:	n/a	n/a
3	POLR2A	chr15:52483435-52484150	MCF-7	breast:	n/a	n/a
4	POLR2A	chr15:52483462-52483811	ECC-1	luminal epithelium:	n/a	n/a
5	TAL1	chr15:52483564-52483770	K562	blood:	n/a	n/a
6	CTCF	chr15:52483523-52483759	K562	blood:	n/a	n/a
7	E2F6	chr15:52483448-52483674	K562	blood:	n/a	n/a
8	CTCF	chr15:52483540-52483690	HRPEpiC	eye:	n/a	n/a
9	MYC	chr15:52483554-52483646	K562	blood:	n/a	n/a
10	MAX	chr15:52483499-52483687	K562	blood:	n/a	n/a
11	CTCF	chr15:52483553-52483795	Medullo	brain:	n/a	n/a
12	MAX	chr15:52483377-52483743	K562	blood:	n/a	n/a
13	CTCF	chr15:52483540-52483690	NHEK	skin:	n/a	n/a
14	CTCF	chr15:52483560-52483710	WERI-Rb-1	eye:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52469254..52473137-chr15:52482082..52484822,3	MCF-7	breast:
2	chr15:52472278..52474319-chr15:52482944..52484455,2	K562	blood:

No data

Variant related genes	Relation type
GNB5	TF binding region
ENSG00000259577	Chromatin interaction
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1063902	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7162283	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8026828	0.83[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11070883	XIRP2	trans	cerebellum	SCAN
rs11070883	LEO1	cis	parietal	SCAN
rs11070883	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52473000-52483800	Weak transcription	A549	lung
2	chr15:52473000-52489000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:52473200-52483600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:52473200-52483600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:52473200-52483800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:52473200-52513600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:52473400-52483600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:52473400-52485600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:52473400-52496400	Weak transcription	Brain Anterior Caudate	brain
10	chr15:52473400-52496400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:52473400-52496600	Weak transcription	Spleen	Spleen
12	chr15:52473600-52512400	Weak transcription	Primary B cells from cord blood	blood
13	chr15:52474600-52488400	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:52475400-52483600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:52475800-52505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:52476800-52484200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:52477600-52497000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr15:52477600-52497200	Weak transcription	Stomach Mucosa	stomach
19	chr15:52477800-52488000	Weak transcription	Gastric	stomach
20	chr15:52477800-52494800	Weak transcription	Fetal Intestine Large	intestine
21	chr15:52478000-52496200	Weak transcription	Liver	Liver
22	chr15:52478600-52488400	Weak transcription	Aorta	Aorta
23	chr15:52479600-52487400	Weak transcription	HepG2	liver
24	chr15:52479600-52495400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:52479600-52496400	Weak transcription	Esophagus	oesophagus
26	chr15:52479800-52483600	Weak transcription	Pancreas	Pancrea
27	chr15:52479800-52485600	Weak transcription	Ovary	ovary
28	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
29	chr15:52481400-52485600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:52481600-52496600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:52482000-52483600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:52482000-52485600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:52482600-52496200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:52482800-52483600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:52483400-52483600	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr15:52483400-52483600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:52483400-52483800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:52483400-52483800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:52483400-52484000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr15:52483400-52484200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:52483400-52484200	Strong transcription	Fetal Intestine Small	intestine
42	chr15:52483400-52492400	Strong transcription	Rectal Mucosa Donor 29	rectum

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