Variant report

Variant	rs835115
Chromosome Location	chr5:14957847-14957848
allele	C/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	SMC3	chr5:14957590-14957881	GM12878	blood:	n/a	n/a
2	CTCF	chr5:14957820-14957970	GM12870	blood:	n/a	n/a
3	RAD21	chr5:14957479-14957942	HepG2	liver:	n/a	chr5:14957729-14957741 chr5:14957731-14957740
4	CTCF	chr5:14957565-14957897	GM12878	blood:	n/a	chr5:14957730-14957746 chr5:14957731-14957752 chr5:14957733-14957740 chr5:14957729-14957747
5	ZNF384	chr5:14957588-14957926	K562	blood:	n/a	n/a
6	STAT3	chr5:14957723-14957857	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr5:14957780-14957930	A549	lung:	n/a	n/a
8	CTCF	chr5:14957492-14957945	HCT-116	colon:	n/a	chr5:14957730-14957746 chr5:14957731-14957752 chr5:14957733-14957740 chr5:14957729-14957747
9	CTCF	chr5:14957579-14957858	Spleen_OC	spleen:	n/a	chr5:14957730-14957746 chr5:14957731-14957752 chr5:14957733-14957740 chr5:14957729-14957747
10	CTCF	chr5:14957426-14957930	A549	lung:	n/a	chr5:14957730-14957746 chr5:14957731-14957752 chr5:14957733-14957740 chr5:14957729-14957747
11	RAD21	chr5:14957578-14957874	Hela-S3	cervix:	n/a	chr5:14957729-14957741 chr5:14957731-14957740
12	CTCF	chr5:14957601-14957859	K562	blood:	n/a	chr5:14957730-14957746 chr5:14957731-14957752 chr5:14957733-14957740 chr5:14957729-14957747
13	RAD21	chr5:14957473-14957908	HCT-116	colon:	n/a	chr5:14957729-14957741 chr5:14957731-14957740

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	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3006072	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006073	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs706297	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs706298	0.88[EUR][1000 genomes]
rs706299	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs706300	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs835066	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835067	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835068	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835069	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835070	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835071	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835072	0.88[EUR][1000 genomes]
rs835078	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835079	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs835080	0.88[EUR][1000 genomes]
rs835085	0.88[EUR][1000 genomes]
rs835086	0.86[EUR][1000 genomes]
rs835087	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835088	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs835089	0.88[EUR][1000 genomes]
rs835090	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs835091	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs835093	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs835096	0.88[EUR][1000 genomes]
rs835097	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs835098	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs835100	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs835108	0.88[EUR][1000 genomes]
rs835109	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835110	0.88[EUR][1000 genomes]
rs835111	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835113	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835114	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835116	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835117	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835118	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs835119	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs856529	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856530	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860664	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs861339	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs863879	0.83[AFR][1000 genomes];0.95[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:8 , 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	chr5:14957200-14958200	Weak transcription	HepG2	liver
4	chr5:14957200-14958400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:14957400-14958800	Enhancers	Hela-S3	cervix
6	chr5:14957400-14961000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:14957600-14959400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:14957600-14959400	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links