Variant report

Variant	rs13357862
Chromosome Location	chr5:114882453-114882454
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	MYC	chr5:114882406-114882573	MCF-7	breast:	n/a	n/a
2	MYC	chr5:114882364-114882518	MCF-7	breast:	n/a	n/a
3	POLR2A	chr5:114882430-114882527	MCF-7	breast:	n/a	n/a
4	POLR2A	chr5:114882411-114882551	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
FEM1C	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10038493	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10041776	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10043094	0.82[ASN][1000 genomes]
rs10053572	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10073505	0.84[ASN][1000 genomes]
rs1015812	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13177180	0.82[ASN][1000 genomes]
rs13184723	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13356084	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2546484	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs256938	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs256977	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256989	0.87[ASN][1000 genomes]
rs256995	0.86[ASN][1000 genomes]
rs372702	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6860557	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6878790	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6892071	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6893854	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6894123	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs746566	0.83[ASN][1000 genomes]
rs766454	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9326964	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1032234	chr5:114785557-114911527	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv3428371	chr5:114880442-114882878	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 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	chr5:114881000-114886400	Weak transcription	Stomach Mucosa	stomach
2	chr5:114881000-114893200	Weak transcription	Right Ventricle	heart
3	chr5:114881200-114887200	Weak transcription	NH-A	brain
4	chr5:114881400-114886400	Weak transcription	Fetal Lung	lung
5	chr5:114881400-114886800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:114882200-114882600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:114882400-114882600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:114882400-114883000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links