Variant report

Variant	rs11783209
Chromosome Location	chr8:125575803-125575804
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	ESR1	chr8:125575518-125576196	T-47D	breast:	n/a	n/a
2	MXI1	chr8:125575625-125576185	HepG2	liver:	n/a	chr8:125575708-125575717
3	FOXA1	chr8:125575576-125576185	T-47D	breast:	n/a	chr8:125576004-125576019 chr8:125575982-125575997
4	FOXA1	chr8:125575692-125576167	HepG2	liver:	n/a	chr8:125576004-125576019 chr8:125575982-125575997
5	FOSL2	chr8:125575774-125576184	HepG2	liver:	n/a	n/a
6	SP1	chr8:125575739-125576130	HepG2	liver:	n/a	n/a
7	FOSL2	chr8:125575745-125576349	MCF-7	breast:	n/a	n/a
8	FOXA1	chr8:125575760-125576232	T-47D	breast:	n/a	chr8:125576004-125576019 chr8:125575982-125575997
9	MAFF	chr8:125575754-125575950	HepG2	liver:	n/a	n/a
10	FOXA2	chr8:125575470-125576393	HepG2	liver:	n/a	n/a
11	GATA3	chr8:125575521-125576275	T-47D	breast:	n/a	n/a
12	ESR1	chr8:125575515-125576233	T-47D	breast:	n/a	n/a
13	GATA3	chr8:125575552-125576244	T-47D	breast:	n/a	n/a
14	MBD4	chr8:125575748-125576165	HepG2	liver:	n/a	n/a
15	ESR1	chr8:125575526-125576177	T-47D	breast:	n/a	n/a
16	EP300	chr8:125575698-125576276	T-47D	breast:	n/a	chr8:125576028-125576035 chr8:125575987-125575997 chr8:125576005-125576015
17	FOXA1	chr8:125575693-125576283	HepG2	liver:	n/a	chr8:125576004-125576019 chr8:125575982-125575997
18	MYBL2	chr8:125575543-125576229	HepG2	liver:	n/a	n/a
19	MAX	chr8:125575417-125576297	HepG2	liver:	n/a	n/a
20	MAX	chr8:125575095-125576266	MCF-7	breast:	n/a	n/a
21	NFIC	chr8:125575578-125576188	HepG2	liver:	n/a	n/a
22	POLR2A	chr8:125575632-125575898	HepG2	liver:	n/a	n/a
23	POLR2A	chr8:125575278-125575831	HepG2	liver:	n/a	n/a
24	EP300	chr8:125575429-125576314	T-47D	breast:	n/a	chr8:125576028-125576035 chr8:125575987-125575997 chr8:125576005-125576015
25	MAFK	chr8:125575692-125576083	HepG2	liver:	n/a	n/a
26	FOXA1	chr8:125575668-125576282	HepG2	liver:	n/a	chr8:125576004-125576019 chr8:125575982-125575997
27	ESR1	chr8:125575496-125576161	T-47D	breast:	n/a	n/a
28	ESR1	chr8:125575742-125576153	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:125560928..125566588-chr8:125566852..125577107,17	MCF-7	breast:
2	chr8:125572673..125575871-chr8:125577015..125582400,6	K562	blood:
3	chr8:125549460..125555106-chr8:125573452..125578755,9	MCF-7	breast:
4	chr8:125573757..125577202-chr8:125578987..125583404,3	MCF-7	breast:
5	chr8:125575430..125576994-chr8:125827635..125829466,2	K562	blood:
6	chr8:125569223..125571926-chr8:125574045..125576529,2	K562	blood:
7	chr8:125486165..125488789-chr8:125574025..125577553,3	MCF-7	breast:
8	chr8:125572972..125577628-chr8:125578200..125582090,6	MCF-7	breast:
9	chr8:125574370..125578079-chr8:125630160..125632086,3	MCF-7	breast:
10	chr8:125567601..125570100-chr8:125573465..125576752,3	MCF-7	breast:

Variant related genes	Relation type
MTSS1	TF binding region
ENSG00000147684	Chromatin interaction
ENSG00000170873	Chromatin interaction
ENSG00000245149	Chromatin interaction
ENSG00000255491	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000170881	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10094916	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10099056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10103773	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs10110655	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12546733	0.92[EUR][1000 genomes]
rs13255599	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13256399	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16899688	0.85[CEU][hapmap]
rs17371123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2303955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750232	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3763540	0.93[ASN][1000 genomes]
rs3763541	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3763542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3763543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[ASN][1000 genomes]
rs3763544	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3829035	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4489311	1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6415485	0.88[EUR][1000 genomes]
rs6470253	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs6470254	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs6997175	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6997184	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs6998600	0.92[EUR][1000 genomes]
rs7010757	0.86[TSI][hapmap]
rs7015228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7015374	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7821954	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7835397	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7841224	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs7846270	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv465801	chr8:125565328-125576681	Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv612145	chr8:125565328-125576681	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv525649	chr8:125565328-125600818	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv465802	chr8:125570144-125576681	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv612146	chr8:125570144-125576681	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv971700	chr8:125575569-125576444	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv1024804	chr8:125575803-125600950	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11783209	TRMT12	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
2	chr8:125554200-125576200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr8:125554400-125576200	Strong transcription	Fetal Intestine Large	intestine
4	chr8:125556800-125576800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:125564400-125576800	Strong transcription	Fetal Intestine Small	intestine
6	chr8:125566000-125576400	Weak transcription	GM12878-XiMat	blood
7	chr8:125566000-125602400	Weak transcription	Aorta	Aorta
8	chr8:125566200-125590400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:125566400-125577600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr8:125566400-125577800	Weak transcription	Small Intestine	intestine
11	chr8:125566400-125600600	Weak transcription	NHEK	skin
12	chr8:125566600-125576400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr8:125566600-125577200	Weak transcription	Osteobl	bone
14	chr8:125566800-125581400	Weak transcription	HSMM	muscle
15	chr8:125567000-125590200	Weak transcription	Fetal Brain Male	brain
16	chr8:125567200-125576200	Weak transcription	Fetal Heart	heart
17	chr8:125568200-125577000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:125568600-125576400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr8:125568800-125576400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr8:125570000-125584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr8:125570800-125605000	Weak transcription	Colon Smooth Muscle	Colon
22	chr8:125571800-125581200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:125572000-125577000	Weak transcription	NHLF	lung
24	chr8:125572400-125576400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr8:125574200-125576000	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr8:125574200-125576000	Weak transcription	Colonic Mucosa	Colon
27	chr8:125574200-125576000	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr8:125574200-125576200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr8:125574200-125577200	Enhancers	Psoas Muscle	Psoas
30	chr8:125574400-125609400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr8:125574800-125576000	Enhancers	Primary T cells fromperipheralblood	blood
32	chr8:125574800-125580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:125574800-125581000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr8:125574800-125590200	Weak transcription	HMEC	breast
35	chr8:125575000-125576000	Enhancers	Fetal Lung	lung
36	chr8:125575000-125576200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr8:125575000-125576200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr8:125575000-125576400	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr8:125575000-125576400	Enhancers	Pancreas	Pancrea
40	chr8:125575000-125576600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr8:125575000-125576600	Enhancers	Right Atrium	heart
42	chr8:125575200-125576000	Enhancers	Thymus	Thymus
43	chr8:125575200-125576200	Enhancers	Fetal Thymus	thymus
44	chr8:125575200-125576400	Enhancers	Primary hematopoietic stem cells	blood
45	chr8:125575200-125576400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr8:125575200-125576400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr8:125575200-125576600	Weak transcription	Brain Angular Gyrus	brain
48	chr8:125575200-125576600	Genic enhancers	HepG2	liver
49	chr8:125575200-125576800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr8:125575200-125576800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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