Variant report

Variant	rs988700
Chromosome Location	chr5:114284436-114284437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10035313	0.95[ASN][1000 genomes]
rs10039613	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap]
rs10054099	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10055057	0.90[EUR][1000 genomes]
rs10055511	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10068274	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10077812	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10477524	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10478216	0.95[ASN][1000 genomes]
rs11749339	0.94[ASN][1000 genomes]
rs11749427	0.94[ASN][1000 genomes]
rs12518615	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12651795	0.93[ASN][1000 genomes]
rs1453026	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2416394	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2416395	0.88[EUR][1000 genomes]
rs4705685	0.85[EUR][1000 genomes]
rs4705687	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55726828	0.86[EUR][1000 genomes]
rs55769443	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55886343	0.86[EUR][1000 genomes]
rs56381271	0.86[EUR][1000 genomes]
rs66578808	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs921595	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9326935	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9326936	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9326938	0.90[ASN][1000 genomes]
rs9326939	0.80[AMR][1000 genomes];0.94[ASN][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	nsv882729	chr5:113743628-114497708	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1020798	chr5:113821828-114392727	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537867	chr5:113821828-114392727	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv4963	chr5:114234431-114288397	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv1808445	chr5:114255927-114327073	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv830453	chr5:114277261-114546536	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs988700	APOD	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114283400-114288000	Enhancers	Fetal Brain Male	brain
2	chr5:114283600-114296400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:114283800-114285200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr5:114284400-114285200	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links