Variant report

Variant	rs13106539
Chromosome Location	chr4:9797703-9797704
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	POLR2A	chr4:9797631-9797972	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RNA5SP154	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10003216	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10004319	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10012516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10013858	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10015665	0.85[EUR][1000 genomes]
rs10022923	0.88[EUR][1000 genomes]
rs10033951	0.81[CEU][hapmap]
rs11726288	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11731100	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12507861	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12509511	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13112576	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13118112	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13124141	0.88[EUR][1000 genomes]
rs13124305	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13129487	0.88[EUR][1000 genomes]
rs13129974	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13141706	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13143667	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13145337	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13145733	0.83[EUR][1000 genomes]
rs13148356	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1519097	0.83[EUR][1000 genomes]
rs1850732	0.83[EUR][1000 genomes]
rs2280206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280207	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280333	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56139970	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6835741	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6841397	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7655090	0.81[CEU][hapmap]
rs7656342	0.90[EUR][1000 genomes]
rs7679464	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7685396	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9685427	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533218	chr4:9371016-10252290	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
2	esv2754610	chr4:9372303-9804524	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv530090	chr4:9383695-10165033	Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
4	nsv1012621	chr4:9456977-9802366	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1012634	chr4:9461218-9802366	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv998043	chr4:9496282-9830208	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
7	nsv878667	chr4:9543673-9903121	ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1014216	chr4:9713612-10223836	Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
9	nsv1010249	chr4:9716101-10086188	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
10	nsv878671	chr4:9766888-9912101	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv964032	chr4:9784827-9802611	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
12	nsv878672	chr4:9786732-10008305	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv878673	chr4:9794724-9834107	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv878674	chr4:9797703-9900314	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv878675	chr4:9797703-9915741	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv878676	chr4:9797703-9978094	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv878677	chr4:9797703-10008305	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13106539	SLC2A9	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:9794400-9798000	Weak transcription	HMEC	breast
2	chr4:9794600-9805800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:9794600-9812600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:9797200-9806400	Weak transcription	HepG2	liver

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