Variant report

Variant	rs2742521
Chromosome Location	chr11:8928704-8928705
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	REST	chr11:8927985-8928722	A549	lung:	n/a	n/a
2	TCF12	chr11:8927956-8928852	ECC-1	luminal epithelium:	n/a	n/a
3	PBX3	chr11:8928005-8928738	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr11:8927946-8928873	SK-N-SH	brain:	n/a	n/a
5	JUN	chr11:8928046-8928861	Hela-S3	cervix:	n/a	chr11:8928350-8928360 chr11:8928317-8928330 chr11:8928351-8928359 chr11:8928351-8928358 chr11:8928557-8928566 chr11:8928244-8928253 chr11:8928352-8928363 chr11:8928351-8928359 chr11:8928350-8928360 chr11:8928350-8928360
6	CEBPB	chr11:8928088-8928730	HCT-116	colon:	n/a	chr11:8928635-8928646 chr11:8928212-8928225
7	NFIC	chr11:8928101-8928830	ECC-1	luminal epithelium:	n/a	n/a
8	ELK4	chr11:8928410-8928797	Hela-S3	cervix:	n/a	n/a
9	TCF12	chr11:8927869-8928892	A549	lung:	n/a	n/a
10	FOSL2	chr11:8927982-8928724	A549	lung:	n/a	chr11:8928350-8928360 chr11:8928351-8928359 chr11:8928351-8928358 chr11:8928557-8928566 chr11:8928244-8928253 chr11:8928352-8928363 chr11:8928351-8928359 chr11:8928350-8928360 chr11:8928350-8928360
11	ATF3	chr11:8928117-8928721	A549	lung:	n/a	chr11:8928318-8928331
12	RXRA	chr11:8928033-8928739	SK-N-SH	brain:	n/a	n/a
13	JUND	chr11:8928086-8928869	Hela-S3	cervix:	n/a	chr11:8928349-8928360 chr11:8928350-8928360 chr11:8928351-8928359 chr11:8928351-8928358 chr11:8928557-8928566 chr11:8928244-8928253 chr11:8928352-8928363 chr11:8928351-8928359 chr11:8928350-8928360 chr11:8928350-8928360
14	STAT3	chr11:8928054-8928801	Hela-S3	cervix:	n/a	chr11:8928225-8928239 chr11:8928226-8928237 chr11:8928557-8928565
15	FOSL2	chr11:8928038-8928756	SK-N-SH	brain:	n/a	chr11:8928350-8928360 chr11:8928351-8928359 chr11:8928351-8928358 chr11:8928557-8928566 chr11:8928244-8928253 chr11:8928352-8928363 chr11:8928351-8928359 chr11:8928350-8928360 chr11:8928350-8928360
16	GATA3	chr11:8926904-8928900	SK-N-SH	brain:	n/a	chr11:8928352-8928361 chr11:8928734-8928745
17	PBX3	chr11:8928143-8928755	A549	lung:	n/a	n/a
18	SP1	chr11:8928018-8928790	A549	lung:	n/a	n/a
19	JUND	chr11:8928010-8928774	SK-N-SH	brain:	n/a	chr11:8928349-8928360 chr11:8928350-8928360 chr11:8928351-8928359 chr11:8928351-8928358 chr11:8928557-8928566 chr11:8928244-8928253 chr11:8928352-8928363 chr11:8928351-8928359 chr11:8928350-8928360 chr11:8928350-8928360
20	RCOR1	chr11:8928118-8928808	Hela-S3	cervix:	n/a	n/a
21	STAT3	chr11:8928023-8929139	MCF10A-Er-Src	breast:	n/a	chr11:8928225-8928239 chr11:8929109-8929120 chr11:8928226-8928237 chr11:8928557-8928565
22	EP300	chr11:8928061-8928857	SK-N-SH	brain:	n/a	chr11:8928322-8928330 chr11:8928061-8928075 chr11:8928317-8928331 chr11:8928351-8928360 chr11:8928555-8928564
23	POLR2A	chr11:8928166-8928720	HUVEC	blood vessel:	n/a	n/a
24	MAX	chr11:8928128-8928729	A549	lung:	n/a	chr11:8928351-8928360 chr11:8928320-8928329
25	EP300	chr11:8928128-8928780	ECC-1	luminal epithelium:	n/a	chr11:8928322-8928330 chr11:8928317-8928331 chr11:8928351-8928360 chr11:8928555-8928564
26	TCF12	chr11:8927989-8928858	SK-N-SH	brain:	n/a	n/a
27	SRF	chr11:8928070-8928713	ECC-1	luminal epithelium:	n/a	n/a
28	JUND	chr11:8927967-8928794	SK-N-SH	brain:	n/a	chr11:8928349-8928360 chr11:8928350-8928360 chr11:8928351-8928359 chr11:8928351-8928358 chr11:8928557-8928566 chr11:8928244-8928253 chr11:8928352-8928363 chr11:8928351-8928359 chr11:8928350-8928360 chr11:8928350-8928360
29	MAFK	chr11:8928129-8928932	Hela-S3	cervix:	n/a	n/a
30	CEBPB	chr11:8928017-8928749	A549	lung:	n/a	chr11:8928635-8928646 chr11:8928212-8928225
31	GATA3	chr11:8927940-8928792	SK-N-SH	brain:	n/a	chr11:8928352-8928361 chr11:8928734-8928745
32	NFIC	chr11:8928140-8928770	SK-N-SH	brain:	n/a	n/a
33	EP300	chr11:8927974-8928773	A549	lung:	n/a	chr11:8928058-8928072 chr11:8928322-8928330 chr11:8928057-8928071 chr11:8928061-8928075 chr11:8928059-8928073 chr11:8928317-8928331 chr11:8928351-8928360 chr11:8928060-8928074 chr11:8928555-8928564
34	TEAD4	chr11:8928105-8928787	ECC-1	luminal epithelium:	n/a	n/a
35	BRCA1	chr11:8928112-8928908	Hela-S3	cervix:	n/a	n/a
36	TCF12	chr11:8928025-8928842	SK-N-SH	brain:	n/a	n/a
37	TEAD4	chr11:8928227-8928729	ECC-1	luminal epithelium:	n/a	n/a
38	CEBPB	chr11:8928002-8928733	Hela-S3	cervix:	n/a	chr11:8928635-8928646 chr11:8928212-8928225
39	NFIC	chr11:8928014-8928888	SK-N-SH	brain:	n/a	n/a
40	TBP	chr11:8928093-8928753	Hela-S3	cervix:	n/a	n/a
41	RFX5	chr11:8928081-8928811	Hela-S3	cervix:	n/a	n/a
42	FOXM1	chr11:8928084-8928821	ECC-1	luminal epithelium:	n/a	n/a
43	STAT3	chr11:8928015-8928752	MCF10A-Er-Src	breast:	n/a	chr11:8928225-8928239 chr11:8928226-8928237 chr11:8928557-8928565
44	NFIC	chr11:8928012-8928884	ECC-1	luminal epithelium:	n/a	n/a
45	FOSL1	chr11:8928113-8928787	HCT-116	colon:	n/a	chr11:8928350-8928360 chr11:8928351-8928359 chr11:8928351-8928358 chr11:8928557-8928566 chr11:8928244-8928253 chr11:8928352-8928363 chr11:8928351-8928359 chr11:8928350-8928360 chr11:8928350-8928360
46	ZBTB33	chr11:8928102-8928709	SK-N-SH	brain:	n/a	n/a
47	FOSL2	chr11:8928142-8928710	SK-N-SH	brain:	n/a	chr11:8928350-8928360 chr11:8928351-8928359 chr11:8928351-8928358 chr11:8928557-8928566 chr11:8928244-8928253 chr11:8928352-8928363 chr11:8928351-8928359 chr11:8928350-8928360 chr11:8928350-8928360
48	EP300	chr11:8927940-8928868	A549	lung:	n/a	chr11:8928058-8928072 chr11:8928322-8928330 chr11:8928057-8928071 chr11:8928061-8928075 chr11:8928059-8928073 chr11:8928317-8928331 chr11:8928351-8928360 chr11:8928060-8928074 chr11:8928555-8928564
49	EP300	chr11:8928083-8928760	Hela-S3	cervix:	n/a	chr11:8928322-8928330 chr11:8928317-8928331 chr11:8928351-8928360 chr11:8928555-8928564
50	GATA3	chr11:8927869-8928909	A549	lung:	n/a	chr11:8928352-8928361 chr11:8928734-8928745

No.	Distal block	Cell Line	Cell type
1	chr11:8922103..8924731-chr11:8927642..8930308,2	K562	blood:
2	chr11:8709093..8712035-chr11:8927581..8930062,2	MCF-7	breast:
3	chr11:8925893..8928872-chr11:8930220..8933061,3	MCF-7	breast:

Variant related genes	Relation type
AKIP1	TF binding region
ENSG00000166444	Chromatin interaction
ENSG00000166452	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10219366	0.91[EUR][1000 genomes]
rs1025438	0.86[JPT][hapmap]
rs10734639	0.91[CEU][hapmap]
rs10769974	0.91[CEU][hapmap]
rs10769976	0.92[EUR][1000 genomes]
rs10769977	0.92[CEU][hapmap]
rs10840150	0.83[EUR][1000 genomes]
rs10840151	0.91[CEU][hapmap]
rs10840154	0.91[CEU][hapmap]
rs10840156	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11042121	0.85[EUR][1000 genomes]
rs12798311	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2016844	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2056903	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2116510	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2116511	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs2163625	0.91[CEU][hapmap]
rs2246878	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2247038	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2568029	0.85[YRI][hapmap]
rs2568034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2568069	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2568074	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2568075	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2568077	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2568079	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2568081	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs2568086	0.91[EUR][1000 genomes]
rs2653556	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2653560	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2653562	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2653587	0.84[EUR][1000 genomes]
rs2653601	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2653604	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2653611	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2742487	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs2742488	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs2742491	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs2742493	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs2742495	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2742496	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2742497	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2742504	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2742505	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2742512	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2742513	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2742514	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2742519	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2742520	0.83[EUR][1000 genomes]
rs3751063	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3751066	0.92[CEU][hapmap]
rs3751068	0.91[CEU][hapmap]
rs3763911	0.96[CEU][hapmap]
rs3763912	0.95[CEU][hapmap]
rs4909951	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4910068	0.82[YRI][hapmap]
rs4910181	0.87[EUR][1000 genomes]
rs7106539	0.85[EUR][1000 genomes]
rs7117900	0.87[YRI][hapmap]
rs909464	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9300096	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs982273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2742521	C11orf17	cis	multi-tissue	Pritchard
rs2742521	C11orf17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8926000-8929400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:8926600-8929000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:8926600-8929000	Enhancers	Muscle Satellite Cultured Cells	--
4	chr11:8926600-8929000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:8926600-8929000	Enhancers	HMEC	breast
6	chr11:8926600-8930000	Enhancers	NHEK	skin
7	chr11:8926800-8929400	Enhancers	NHLF	lung
8	chr11:8927000-8928800	Enhancers	HSMMtube	muscle
9	chr11:8927000-8929000	Enhancers	Osteobl	bone
10	chr11:8927200-8928800	Enhancers	HSMM	muscle
11	chr11:8927200-8929000	Enhancers	NHDF-Ad	bronchial
12	chr11:8927200-8931000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:8927400-8929000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:8927600-8929000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr11:8928000-8929000	Enhancers	HUVEC	blood vessel
16	chr11:8928400-8928800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:8928400-8928800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:8928400-8928800	Flanking Active TSS	A549	lung
19	chr11:8928400-8929400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:8928600-8928800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:8928600-8928800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:8928600-8928800	Enhancers	NH-A	brain
23	chr11:8928600-8929000	Flanking Active TSS	Hela-S3	cervix
24	chr11:8928600-8929600	Enhancers	Placenta	Placenta

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