Variant report

Variant	rs856529
Chromosome Location	chr5:14959725-14959726
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	STAT3	chr5:14959579-14960073	MCF10A-Er-Src	breast:	n/a	n/a
2	HDAC2	chr5:14959420-14960135	MCF-7	breast:	n/a	n/a
3	POLR2A	chr5:14959351-14959821	Hela-S3	cervix:	n/a	n/a
4	TCF12	chr5:14959438-14960117	A549	lung:	n/a	n/a
5	NR2F2	chr5:14959286-14960200	MCF-7	breast:	n/a	chr5:14959744-14959759
6	HA-E2F1	chr5:14959387-14960028	MCF-7	breast:	n/a	chr5:14959446-14959455
7	MYC	chr5:14959540-14960071	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr5:14959587-14960018	MCF10A-Er-Src	breast:	n/a	n/a
9	FOXA2	chr5:14959515-14959970	A549	lung:	n/a	chr5:14959798-14959810
10	BHLHE40	chr5:14959568-14959781	HepG2	liver:	n/a	n/a
11	MAX	chr5:14959135-14960573	Hela-S3	cervix:	n/a	chr5:14960269-14960278
12	ZKSCAN1	chr5:14959348-14960155	Hela-S3	cervix:	n/a	n/a
13	FOS	chr5:14959588-14960051	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr5:14959580-14960048	MCF10A-Er-Src	breast:	n/a	n/a
15	TCF7L2	chr5:14958988-14960993	Hela-S3	cervix:	n/a	chr5:14959745-14959752 chr5:14959069-14959076
16	SMARCC1	chr5:14959195-14960257	Hela-S3	cervix:	n/a	n/a
17	MAX	chr5:14959458-14960169	MCF-7	breast:	n/a	n/a
18	GTF3C2	chr5:14958810-14960034	Hela-S3	cervix:	n/a	n/a
19	RFX5	chr5:14959203-14960207	Hela-S3	cervix:	n/a	n/a
20	STAT3	chr5:14959327-14960055	Hela-S3	cervix:	n/a	chr5:14959578-14959586
21	SMARCC2	chr5:14959210-14960183	Hela-S3	cervix:	n/a	n/a
22	MYC	chr5:14959234-14960297	Hela-S3	cervix:	n/a	chr5:14960269-14960278
23	TFAP2C	chr5:14959211-14960694	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr5:14959240-14959921	Hela-S3	cervix:	n/a	n/a
25	TFAP2A	chr5:14959390-14959885	Hela-S3	cervix:	n/a	chr5:14959556-14959571
26	HA-E2F1	chr5:14959524-14959875	Hela-S3	cervix:	n/a	n/a
27	STAT3	chr5:14959547-14960047	MCF10A-Er-Src	breast:	n/a	chr5:14959578-14959586
28	FOS	chr5:14959643-14959994	MCF10A-Er-Src	breast:	n/a	n/a
29	EP300	chr5:14958279-14960017	Hela-S3	cervix:	n/a	chr5:14958444-14958453 chr5:14959101-14959111 chr5:14959336-14959346 chr5:14958781-14958790
30	NR2F2	chr5:14959442-14960049	MCF-7	breast:	n/a	chr5:14959744-14959759
31	E2F4	chr5:14959657-14959862	MCF10A-Er-Src	breast:	n/a	n/a
32	MAX	chr5:14959373-14960398	A549	lung:	n/a	chr5:14960269-14960278
33	HDAC2	chr5:14959512-14959928	MCF-7	breast:	n/a	n/a
34	MAX	chr5:14959509-14959913	HepG2	liver:	n/a	n/a
35	ELK1	chr5:14959403-14959987	Hela-S3	cervix:	n/a	n/a
36	BRCA1	chr5:14959305-14960017	Hela-S3	cervix:	n/a	n/a
37	MAFK	chr5:14959103-14960081	Hela-S3	cervix:	n/a	n/a
38	MAX	chr5:14959255-14960249	Hela-S3	cervix:	n/a	n/a
39	GTF2F1	chr5:14959206-14960212	Hela-S3	cervix:	n/a	n/a
40	FOSL2	chr5:14959221-14960089	A549	lung:	n/a	n/a
41	USF2	chr5:14959331-14960116	Hela-S3	cervix:	n/a	n/a
42	GATA3	chr5:14959368-14960131	MCF-7	breast:	n/a	chr5:14959655-14959668
43	FOXA2	chr5:14959616-14960045	A549	lung:	n/a	chr5:14959798-14959810
44	CHD2	chr5:14959220-14960136	Hela-S3	cervix:	n/a	n/a
45	CEBPB	chr5:14958217-14960214	Hela-S3	cervix:	n/a	n/a
46	MXI1	chr5:14959182-14960119	Hela-S3	cervix:	n/a	n/a
47	FOSL2	chr5:14959478-14960004	MCF-7	breast:	n/a	n/a
48	FOSL2	chr5:14959614-14959928	A549	lung:	n/a	n/a
49	GATA3	chr5:14959285-14960019	MCF-7	breast:	n/a	chr5:14959655-14959668
50	E2F6	chr5:14959450-14960295	A549	lung:	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	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3006072	0.93[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]
rs3006073	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]
rs706297	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs706298	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs706299	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs706300	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs835066	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835067	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835068	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835069	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835070	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835071	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835072	0.90[EUR][1000 genomes]
rs835078	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835079	0.86[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];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835088	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835089	0.90[EUR][1000 genomes]
rs835090	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs835091	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs835093	0.81[AMR][1000 genomes];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	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs835100	0.94[CEU][hapmap];0.93[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs835108	0.90[EUR][1000 genomes]
rs835109	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835110	0.93[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs835111	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835113	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835114	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835115	0.95[AFR][1000 genomes];0.97[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];0.86[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];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs835119	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs856530	0.86[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];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861339	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863879	0.86[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:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14957400-14961000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:14958000-14960600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:14958200-14960000	Enhancers	HepG2	liver
4	chr5:14958200-14960000	Enhancers	Osteobl	bone
5	chr5:14958200-14960600	Enhancers	HMEC	breast
6	chr5:14958600-14959800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:14958800-14960800	Flanking Active TSS	Hela-S3	cervix
8	chr5:14959200-14960000	Enhancers	Fetal Heart	heart
9	chr5:14959400-14960000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:14959400-14960200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:14959400-14960200	Enhancers	NHEK	skin
12	chr5:14959400-14960400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:14959400-14960400	Flanking Active TSS	A549	lung
14	chr5:14959600-14959800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:14959600-14960600	Enhancers	Esophagus	oesophagus

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