Variant report

Variant	rs10965050
Chromosome Location	chr9:21528058-21528059
allele	G/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	JUND	chr9:21519231-21528507	HCT-116	colon:	n/a	n/a
2	POLR2A	chr9:21519358-21529034	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr9:21526622-21528964	Hela-S3	cervix:	n/a	n/a
4	JUND	chr9:21517910-21528426	HCT-116	colon:	n/a	n/a
5	POLR2A	chr9:21527840-21528234	A549	lung:	n/a	n/a
6	POLR2A	chr9:21515900-21530251	A549	lung:	n/a	n/a
7	POLR2A	chr9:21527603-21528844	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr9:21516566-21534519	HCT-116	colon:	n/a	n/a
9	POLR2A	chr9:21519394-21529027	HCT-116	colon:	n/a	n/a
10	CTCF	chr9:21527920-21528070	AG04450	lung:	n/a	n/a
11	POLR2A	chr9:21527043-21528328	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr9:21527848-21528243	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000264379	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10491567	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10811549	0.85[EUR][1000 genomes]
rs10811551	0.83[EUR][1000 genomes]
rs10811556	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10811557	0.81[AMR][1000 genomes]
rs10811562	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811563	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10811564	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811565	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10811566	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10811568	0.93[ASN][1000 genomes]
rs10965031	0.83[EUR][1000 genomes]
rs10965049	0.99[ASN][1000 genomes]
rs10965053	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10965054	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10965059	0.91[EUR][1000 genomes]
rs10965060	0.84[ASN][1000 genomes]
rs10965063	0.85[EUR][1000 genomes]
rs1125488	0.80[EUR][1000 genomes]
rs12377379	0.91[EUR][1000 genomes]
rs12378286	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12378990	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12379382	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12379709	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12379721	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16938435	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16938448	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2039380	0.81[EUR][1000 genomes]
rs55683539	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55835613	0.91[EUR][1000 genomes]
rs56122777	0.91[EUR][1000 genomes]
rs7026731	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7032680	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7041183	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72703411	0.83[EUR][1000 genomes]
rs72703445	0.91[EUR][1000 genomes]
rs72703447	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72703448	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72703449	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72703450	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9644855	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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	nsv892740	chr9:21471499-21551513	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases
2	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
4	nsv892741	chr9:21517302-21551513	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21507200-21551400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:21508000-21542000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:21516800-21542600	Weak transcription	Stomach Mucosa	stomach
4	chr9:21522600-21532600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:21522600-21533200	Strong transcription	NH-A	brain
6	chr9:21522800-21530000	ZNF genes & repeats	A549	lung
7	chr9:21524400-21532200	Strong transcription	Osteobl	bone
8	chr9:21525600-21534000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:21525800-21530800	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr9:21526200-21532400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:21526400-21529600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:21526400-21530000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:21526400-21534800	Strong transcription	NHEK	skin
14	chr9:21526600-21528600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:21526600-21529000	Strong transcription	HUVEC	blood vessel
16	chr9:21526600-21530200	Strong transcription	HSMM	muscle
17	chr9:21526600-21533000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:21526800-21534800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:21527000-21531000	Strong transcription	NHDF-Ad	bronchial
20	chr9:21527000-21531200	Strong transcription	NHLF	lung
21	chr9:21527400-21528200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
22	chr9:21527400-21528800	Strong transcription	Fetal Intestine Large	intestine
23	chr9:21527400-21529800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:21527600-21528200	Enhancers	Primary B cells from peripheral blood	blood
25	chr9:21527600-21528200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
26	chr9:21527600-21528200	Strong transcription	Fetal Stomach	stomach
27	chr9:21527600-21528400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:21527600-21528600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:21527600-21528800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
30	chr9:21527600-21528800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:21527600-21528800	Strong transcription	Gastric	stomach
32	chr9:21527600-21528800	ZNF genes & repeats	Hela-S3	cervix
33	chr9:21527600-21528800	Genic enhancers	HMEC	breast
34	chr9:21527600-21529000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:21527600-21529000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:21527600-21529000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:21527600-21529800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:21527800-21528400	ZNF genes & repeats	Esophagus	oesophagus
39	chr9:21527800-21528400	Strong transcription	Fetal Intestine Small	intestine
40	chr9:21527800-21528800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:21527800-21528800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:21527800-21529000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:21527800-21536600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:21528000-21528200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr9:21528000-21528400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:21528000-21528800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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