Variant report

Variant	rs11753890
Chromosome Location	chr6:39248886-39248887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39236174..39238959-chr6:39247299..39249650,2	MCF-7	breast:
2	chr6:39246289..39249933-chr6:39249942..39252765,4	MCF-7	breast:
3	chr6:39243650..39250520-chr6:39262135..39271800,15	MCF-7	breast:
4	chr6:39246522..39249278-chr6:39249658..39251560,2	MCF-7	breast:
5	chr6:38980068..38982794-chr6:39247748..39249304,2	K562	blood:
6	chr6:39195713..39197963-chr6:39247882..39249799,3	K562	blood:
7	chr6:39195286..39197963-chr6:39246502..39249488,3	K562	blood:
8	chr6:39191982..39197381-chr6:39245126..39249052,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10947796	0.82[EUR][1000 genomes]
rs10947801	0.91[ASN][1000 genomes]
rs10947802	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11961984	0.81[ASN][1000 genomes]
rs12195376	0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12202277	0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12202455	0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12207643	0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12209091	0.91[ASN][1000 genomes]
rs12210847	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211098	0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12214600	0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13194563	0.81[ASN][1000 genomes]
rs13214473	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1535497	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1885616	0.91[ASN][1000 genomes]
rs1885617	0.91[ASN][1000 genomes]
rs1885618	0.91[ASN][1000 genomes]
rs1885621	0.91[ASN][1000 genomes]
rs2758882	0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2758883	0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs2758884	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2758885	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2758887	0.91[ASN][1000 genomes]
rs2758888	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2758889	0.91[ASN][1000 genomes]
rs2758890	0.91[ASN][1000 genomes]
rs2758891	0.91[ASN][1000 genomes]
rs2758893	0.91[ASN][1000 genomes]
rs2758894	0.91[ASN][1000 genomes]
rs2758895	0.87[ASN][1000 genomes]
rs2758897	0.91[ASN][1000 genomes]
rs2758898	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2758899	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2758900	0.89[JPT][hapmap]
rs2815048	0.91[ASN][1000 genomes]
rs2815049	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2815050	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2815051	0.91[ASN][1000 genomes]
rs2815052	0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2815053	0.84[ASN][1000 genomes]
rs2815054	0.91[ASN][1000 genomes]
rs2815057	0.91[ASN][1000 genomes]
rs36044810	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711593	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4714234	0.80[EUR][1000 genomes]
rs4714235	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59582961	0.89[ASN][1000 genomes]
rs62397166	0.84[ASN][1000 genomes]
rs62397167	0.91[ASN][1000 genomes]
rs62397168	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71556989	0.89[ASN][1000 genomes]
rs734408	0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9462515	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9471040	0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9471043	0.89[JPT][hapmap]
rs9471045	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3358883	chr6:39248522-39248891	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv3365683	chr6:39248539-39249004	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	esv3487482	chr6:39248557-39248977	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	esv3487483	chr6:39248557-39248977	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39240400-39250200	Enhancers	Stomach Mucosa	stomach
2	chr6:39242600-39249600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:39246200-39251000	Enhancers	Liver	Liver
4	chr6:39246800-39250400	Enhancers	Esophagus	oesophagus
5	chr6:39247000-39249000	Enhancers	Duodenum Mucosa	Duodenum
6	chr6:39247000-39250200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:39247000-39250200	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr6:39247000-39250400	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr6:39247200-39249000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:39247200-39250400	Enhancers	Colonic Mucosa	Colon
11	chr6:39247400-39249200	Enhancers	Lung	lung
12	chr6:39247600-39249200	Weak transcription	Gastric	stomach
13	chr6:39247800-39249400	Enhancers	HMEC	breast
14	chr6:39247800-39249600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:39248200-39250200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:39248400-39249400	Weak transcription	Pancreas	Pancrea
17	chr6:39248400-39249400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr6:39248400-39263400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:39248400-39263400	Weak transcription	Right Atrium	heart
20	chr6:39248600-39249000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:39248600-39249000	Weak transcription	Placenta	Placenta
22	chr6:39248600-39249000	Weak transcription	Small Intestine	intestine
23	chr6:39248800-39252800	Weak transcription	Spleen	Spleen

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