Variant report

Variant	rs3006073
Chromosome Location	chr5:14958415-14958416
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	ZNF217	chr5:14958278-14958478	MCF-7	breast:	n/a	n/a
2	MYC	chr5:14958360-14958785	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr5:14958327-14958719	A549	lung:	n/a	n/a
4	RAD21	chr5:14958358-14958681	Hela-S3	cervix:	n/a	n/a
5	FOSL2	chr5:14958196-14958674	A549	lung:	n/a	chr5:14958444-14958453 chr5:14958443-14958453 chr5:14958444-14958451
6	CEBPB	chr5:14958341-14958569	HepG2	liver:	n/a	n/a
7	EP300	chr5:14958279-14960017	Hela-S3	cervix:	n/a	chr5:14958444-14958453 chr5:14959101-14959111 chr5:14959336-14959346 chr5:14958781-14958790
8	CHD2	chr5:14958389-14958664	Hela-S3	cervix:	n/a	n/a
9	TBP	chr5:14958334-14958638	Hela-S3	cervix:	n/a	n/a
10	FOS	chr5:14958284-14958786	MCF10A-Er-Src	breast:	n/a	chr5:14958444-14958453 chr5:14958443-14958453 chr5:14958444-14958451
11	FOS	chr5:14958313-14958683	MCF10A-Er-Src	breast:	n/a	chr5:14958444-14958453 chr5:14958443-14958453 chr5:14958444-14958451
12	STAT3	chr5:14958311-14958783	MCF10A-Er-Src	breast:	n/a	chr5:14958755-14958775 chr5:14958755-14958775 chr5:14958753-14958764
13	GTF2F1	chr5:14958410-14958646	Hela-S3	cervix:	n/a	n/a
14	STAT3	chr5:14958231-14958741	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr5:14958279-14958702	MCF-7	breast:	n/a	n/a
16	JUND	chr5:14958261-14958824	Hela-S3	cervix:	n/a	chr5:14958442-14958453 chr5:14958444-14958453 chr5:14958443-14958453 chr5:14958444-14958451
17	CEBPB	chr5:14958217-14960214	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr5:14958360-14958629	IMR90	lung:	n/a	n/a
19	FOS	chr5:14958275-14958785	MCF10A-Er-Src	breast:	n/a	chr5:14958444-14958453 chr5:14958443-14958453 chr5:14958444-14958451
20	CEBPB	chr5:14958329-14958645	A549	lung:	n/a	n/a
21	MAX	chr5:14958348-14958695	Hela-S3	cervix:	n/a	n/a
22	RCOR1	chr5:14958298-14958705	Hela-S3	cervix:	n/a	n/a
23	FOS	chr5:14958257-14958800	MCF10A-Er-Src	breast:	n/a	chr5:14958444-14958453 chr5:14958443-14958453 chr5:14958444-14958451
24	RFX5	chr5:14958333-14958658	Hela-S3	cervix:	n/a	n/a
25	FOS	chr5:14958237-14958637	Hela-S3	cervix:	n/a	chr5:14958444-14958453 chr5:14958443-14958453 chr5:14958444-14958451
26	STAT3	chr5:14958293-14958856	MCF10A-Er-Src	breast:	n/a	chr5:14958755-14958775 chr5:14958755-14958775 chr5:14958753-14958764
27	STAT3	chr5:14958325-14959000	MCF10A-Er-Src	breast:	n/a	chr5:14958755-14958775 chr5:14958755-14958775 chr5:14958753-14958764
28	SMC3	chr5:14958373-14958697	Hela-S3	cervix:	n/a	n/a
29	STAT3	chr5:14958339-14958659	Hela-S3	cervix:	n/a	n/a
30	E2F4	chr5:14958385-14958682	MCF10A-Er-Src	breast:	n/a	n/a
31	MYC	chr5:14958380-14958727	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SEPHS2P1	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs2591533	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3006072	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706297	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs706298	0.90[EUR][1000 genomes]
rs706299	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs706300	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs835066	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835067	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835068	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835069	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835070	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835071	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835072	0.90[EUR][1000 genomes]
rs835078	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835079	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs835080	0.90[EUR][1000 genomes]
rs835085	0.90[EUR][1000 genomes]
rs835086	0.88[EUR][1000 genomes]
rs835087	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835088	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835089	0.90[EUR][1000 genomes]
rs835090	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs835091	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs835093	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs835096	0.90[EUR][1000 genomes]
rs835097	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs835098	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs835100	0.94[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs835108	0.90[EUR][1000 genomes]
rs835109	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835110	0.93[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs835111	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835113	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835114	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835116	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835117	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs835119	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs856529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856530	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860664	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861339	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863879	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv830212	chr5:14784197-14966683	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv530221	chr5:14859687-15364470	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv432717	chr5:14887400-15126500	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1017579	chr5:14888997-15194335	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv597261	chr5:14913369-14962587	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv881445	chr5:14917813-14960920	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv881333	chr5:14924458-14962587	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv461982	chr5:14943456-15044842	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv597262	chr5:14943456-15044842	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv470991	chr5:14949696-15022112	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr5:14955400-14958600	Weak transcription	Fetal Heart	heart
2	chr5:14957000-14959400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:14957400-14958800	Enhancers	Hela-S3	cervix
4	chr5:14957400-14961000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:14957600-14959400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:14957600-14959400	Enhancers	A549	lung
7	chr5:14958000-14960600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:14958200-14960000	Enhancers	HepG2	liver
9	chr5:14958200-14960000	Enhancers	Osteobl	bone
10	chr5:14958200-14960600	Enhancers	HMEC	breast
11	chr5:14958400-14958600	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links