Variant report

Variant	rs11599300
Chromosome Location	chr10:49880513-49880514
allele	A/C
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	EBF1	chr10:49879018-49881237	GM12878	blood:	n/a	chr10:49880003-49880016
2	POLR2A	chr10:49880072-49880628	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr10:49879045-49881375	GM12892	blood:	n/a	n/a
4	RELA	chr10:49880258-49881399	GM18505	blood:	n/a	n/a
5	YY1	chr10:49880349-49880873	GM12892	blood:	n/a	n/a
6	NFIC	chr10:49879156-49881432	GM12878	blood:	n/a	n/a
7	TCF12	chr10:49879327-49880806	ECC-1	luminal epithelium:	n/a	n/a
8	RUNX3	chr10:49879060-49881274	GM12878	blood:	n/a	n/a
9	BCLAF1	chr10:49879145-49881259	GM12878	blood:	n/a	chr10:49879792-49879801
10	MTA3	chr10:49879026-49881279	GM12878	blood:	n/a	n/a
11	TAF1	chr10:49880330-49880575	GM12892	blood:	n/a	n/a
12	PML	chr10:49879109-49881338	GM12878	blood:	n/a	n/a
13	RELA	chr10:49879186-49881316	GM12878	blood:	n/a	n/a
14	POU2F2	chr10:49880217-49880777	GM12891	blood:	n/a	chr10:49880581-49880589
15	RELA	chr10:49880293-49881207	GM10847	blood:	n/a	n/a
16	CTCF	chr10:49880400-49880550	GM12865	blood:	n/a	n/a
17	PAX5	chr10:49879445-49880690	GM12878	blood:	n/a	n/a
18	CEBPB	chr10:49880424-49881302	GM12878	blood:	n/a	n/a
19	BATF	chr10:49880346-49880607	GM12878	blood:	n/a	n/a
20	MAX	chr10:49879422-49881020	ECC-1	luminal epithelium:	n/a	n/a
21	POU2F2	chr10:49880225-49881019	GM12878	blood:	n/a	chr10:49880581-49880589
22	FOXM1	chr10:49880245-49880899	GM12878	blood:	n/a	n/a
23	ELF1	chr10:49879168-49880655	GM12878	blood:	n/a	chr10:49879765-49879777 chr10:49879725-49879737 chr10:49879783-49879795
24	TAF1	chr10:49880283-49880704	GM12878	blood:	n/a	n/a
25	CTCF	chr10:49880424-49880566	GM12878	blood:	n/a	n/a
26	SMC3	chr10:49879549-49881126	GM12878	blood:	n/a	chr10:49879774-49879784 chr10:49880556-49880566
27	POLR2A	chr10:49879372-49881284	GM12891	blood:	n/a	n/a
28	RELA	chr10:49878945-49881310	GM19099	blood:	n/a	n/a
29	CTCF	chr10:49880400-49880550	GM12868	blood:	n/a	n/a
30	FOXM1	chr10:49880199-49881253	GM12878	blood:	n/a	n/a
31	EBF1	chr10:49879124-49881047	GM12878	blood:	n/a	chr10:49880003-49880016
32	RELA	chr10:49880280-49881122	GM18526	blood:	n/a	n/a
33	RUNX3	chr10:49879263-49881315	GM12878	blood:	n/a	n/a
34	ZEB1	chr10:49880230-49880926	GM12878	blood:	n/a	n/a
35	PAX5	chr10:49880307-49880686	GM12878	blood:	n/a	n/a
36	POLR2A	chr10:49879215-49881217	GM12892	blood:	n/a	n/a
37	POLR2A	chr10:49878832-49881450	Raji	blood:	n/a	n/a
38	USF1	chr10:49880255-49880513	GM12878	blood:	n/a	n/a
39	RELA	chr10:49879057-49881219	GM18951	blood:	n/a	n/a
40	POLR2A	chr10:49880316-49880632	GM12891	blood:	n/a	n/a
41	ZBTB7A	chr10:49879436-49880545	ECC-1	luminal epithelium:	n/a	n/a
42	EBF1	chr10:49880294-49881031	GM12878	blood:	n/a	n/a
43	IRF4	chr10:49879443-49880766	GM12878	blood:	n/a	n/a
44	POLR2A	chr10:49878916-49881435	GM12891	blood:	n/a	n/a
45	POLR2A	chr10:49878788-49881436	GM19099	blood:	n/a	n/a
46	RCOR1	chr10:49879016-49881148	GM12878	blood:	n/a	n/a
47	POLR2A	chr10:49879272-49881234	GM10847	blood:	n/a	n/a
48	USF1	chr10:49880133-49880606	ECC-1	luminal epithelium:	n/a	n/a
49	EP300	chr10:49879331-49880774	ECC-1	luminal epithelium:	n/a	chr10:49879771-49879787 chr10:49880556-49880572
50	NRF1	chr10:49880222-49880583	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000236800	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1004407	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11101420	0.89[ASN][1000 genomes]
rs11101421	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11101423	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11101428	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11101429	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11597062	0.92[ASN][1000 genomes]
rs11598871	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263405	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12762257	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2377608	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4269848	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4838638	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5001509	0.83[ASN][1000 genomes]
rs5001511	0.92[ASN][1000 genomes]
rs56136724	0.92[ASN][1000 genomes]
rs6537571	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67580405	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71500246	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7895383	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49879000-49881600	Flanking Active TSS	GM12878-XiMat	blood
2	chr10:49879200-49880600	Enhancers	Fetal Muscle Leg	muscle
3	chr10:49879400-49880600	Enhancers	Fetal Thymus	thymus
4	chr10:49879400-49881400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr10:49879600-49880600	Enhancers	Esophagus	oesophagus
6	chr10:49880000-49881000	Flanking Active TSS	Primary B cells from peripheral blood	blood
7	chr10:49880200-49880600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:49880200-49881000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:49880200-49881800	Enhancers	Primary B cells from cord blood	blood
10	chr10:49880400-49880600	Bivalent/Poised TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:49880400-49880600	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links