Variant report

Variant	rs2919720
Chromosome Location	chr11:70956937-70956938
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	SP1	chr11:70956887-70957409	H1-hESC	embryonic stem cell:	n/a	chr11:70957344-70957358 chr11:70957345-70957354
2	ATF2	chr11:70956880-70957345	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUND	chr11:70956930-70957162	H1-hESC	embryonic stem cell:	n/a	chr11:70957043-70957057
4	POLR2A	chr11:70956731-70958011	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP1	chr11:70956825-70958084	H1-hESC	embryonic stem cell:	n/a	chr11:70957344-70957358 chr11:70957713-70957727 chr11:70957345-70957354 chr11:70957426-70957439
6	POLR2A	chr11:70956598-70958169	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr11:70956877-70957277	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTBP2	chr11:70956883-70957810	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:70951609..70954007-chr11:70955977..70958754,2	MCF-7	breast:
2	chr11:70932436..70935319-chr11:70956669..70958348,2	MCF-7	breast:
3	chr11:70956574..70959465-chr11:70959988..70966157,6	MCF-7	breast:
4	chr11:70955660..70957378-chr11:70976779..70978996,2	MCF-7	breast:

Variant related genes	Relation type
SHANK2	TF binding region
ENSG00000162105	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1004872	1.00[ASN][1000 genomes]
rs1372108	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985681	1.00[ASN][1000 genomes]
rs2919724	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2919726	1.00[ASN][1000 genomes]
rs2919727	1.00[ASN][1000 genomes]
rs2919728	1.00[ASN][1000 genomes]
rs2919729	1.00[ASN][1000 genomes]
rs2919740	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2919742	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020024	1.00[ASN][1000 genomes]
rs3020025	1.00[ASN][1000 genomes]
rs3020027	1.00[ASN][1000 genomes]
rs3020028	1.00[ASN][1000 genomes]
rs3020032	1.00[ASN][1000 genomes]
rs4078937	0.89[ASN][1000 genomes]
rs60796828	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:70946400-70961600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr11:70952800-70961200	Weak transcription	HSMM	muscle
3	chr11:70953000-70957600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:70953000-70958200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr11:70953000-70959000	Weak transcription	Gastric	stomach
6	chr11:70953000-70959800	Genic enhancers	HepG2	liver
7	chr11:70953200-70957400	Weak transcription	Fetal Lung	lung
8	chr11:70953200-70960200	Weak transcription	Fetal Intestine Large	intestine
9	chr11:70953400-70957800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr11:70953800-70957000	Weak transcription	Pancreas	Pancrea
11	chr11:70954400-70958600	Weak transcription	A549	lung
12	chr11:70955200-70958000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:70955200-70959000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:70955400-70958400	Weak transcription	Liver	Liver
15	chr11:70955600-70958600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:70955800-70957000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:70956000-70957000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:70956000-70959600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:70956000-70960000	Strong transcription	Fetal Intestine Small	intestine
20	chr11:70956400-70959200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr11:70956600-70957000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr11:70956600-70957200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:70956600-70957600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:70956600-70957600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr11:70956600-70957600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr11:70956600-70957600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:70956600-70957600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr11:70956600-70957800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:70956600-70958400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr11:70956600-70958600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr11:70956600-70959400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:70956600-70959400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr11:70956800-70957000	Bivalent Enhancer	Placenta	Placenta
34	chr11:70956800-70957000	Flanking Active TSS	Lung	lung
35	chr11:70956800-70957600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:70956800-70957600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr11:70956800-70957600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr11:70956800-70959000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr11:70956800-70960400	Bivalent Enhancer	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links