Variant report

Variant	rs11575342
Chromosome Location	chr7:50596357-50596358
allele	C/T
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	MAZ	chr7:50596172-50597032	HepG2	liver:	n/a	n/a
2	EP300	chr7:50593552-50596619	SK-N-SH	brain:	n/a	chr7:50596383-50596393
3	FOXA2	chr7:50596093-50596724	HepG2	liver:	n/a	n/a
4	SMC3	chr7:50596238-50596695	HepG2	liver:	n/a	n/a
5	HDAC2	chr7:50596349-50596798	HepG2	liver:	n/a	chr7:50596708-50596722
6	FOXA1	chr7:50596011-50596736	HepG2	liver:	n/a	n/a
7	HNF4G	chr7:50596231-50596781	HepG2	liver:	n/a	chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596588-50596600 chr7:50596586-50596601 chr7:50596587-50596602
8	HNF4A	chr7:50596335-50596784	HepG2	liver:	n/a	chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596588-50596600 chr7:50596586-50596601
9	MYBL2	chr7:50596244-50596743	HepG2	liver:	n/a	n/a
10	POLR2A	chr7:50596308-50596896	HepG2	liver:	n/a	n/a
11	HNF4G	chr7:50596343-50596785	HepG2	liver:	n/a	chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596588-50596600 chr7:50596586-50596601 chr7:50596587-50596602
12	EP300	chr7:50596020-50596813	HepG2	liver:	n/a	chr7:50596383-50596393
13	HNF4A	chr7:50596315-50596760	HepG2	liver:	n/a	chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596588-50596600 chr7:50596586-50596601

Variant related genes	Relation type
ENSG00000226122	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10268819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107743	1.00[JPT][hapmap]
rs11575282	1.00[JPT][hapmap]
rs11575286	1.00[JPT][hapmap]
rs11575298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575300	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575301	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575313	1.00[JPT][hapmap]
rs11575321	1.00[JPT][hapmap]
rs11575322	1.00[JPT][hapmap]
rs11575404	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11575429	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575548	1.00[JPT][hapmap]
rs11575553	1.00[JPT][hapmap]
rs11765109	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770199	1.00[CHB][hapmap]
rs11771818	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11772525	1.00[CHB][hapmap]
rs12718611	0.86[EUR][1000 genomes]
rs1349491	1.00[JPT][hapmap]
rs1466163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17553036	1.00[JPT][hapmap]
rs17553791	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17634717	1.00[JPT][hapmap]
rs17634771	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17634958	1.00[JPT][hapmap]
rs17635123	1.00[JPT][hapmap]
rs2167368	1.00[ASN][1000 genomes]
rs2242041	1.00[JPT][hapmap]
rs2329367	1.00[JPT][hapmap]
rs2329486	1.00[CHB][hapmap]
rs2715126	1.00[JPT][hapmap]
rs2715129	1.00[CHB][hapmap]
rs2876830	1.00[JPT][hapmap]
rs3177656	1.00[JPT][hapmap]
rs3807553	1.00[JPT][hapmap]
rs4947714	1.00[CHB][hapmap]
rs6593002	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952381	1.00[ASN][1000 genomes]
rs6975015	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975747	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73342846	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785984	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810039	1.00[CHB][hapmap]

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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:50589000-50599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:50595000-50597200	Enhancers	Liver	Liver
4	chr7:50595200-50597000	Enhancers	Gastric	stomach
5	chr7:50595200-50600000	Enhancers	Pancreas	Pancrea
6	chr7:50595200-50604600	Genic enhancers	Fetal Intestine Small	intestine
7	chr7:50595800-50597000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr7:50595800-50597400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:50595800-50599400	Enhancers	Fetal Intestine Large	intestine
10	chr7:50596000-50596400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:50596000-50596400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr7:50596000-50596800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:50596000-50597400	Enhancers	Duodenum Mucosa	Duodenum
14	chr7:50596000-50597800	Enhancers	Stomach Mucosa	stomach
15	chr7:50596200-50596800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:50596200-50597000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr7:50596200-50597000	Flanking Active TSS	HepG2	liver
18	chr7:50596200-50598200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:50596200-50598800	Weak transcription	Brain Germinal Matrix	brain
20	chr7:50596200-50599000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:50596200-50599000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:50596200-50599200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links