Variant report

Variant	rs12516794
Chromosome Location	chr5:59561718-59561719
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	REST	chr5:59561603-59562060	PFSK-1	brain:	n/a	chr5:59561837-59561846
2	FOXA1	chr5:59561569-59561958	HepG2	liver:	n/a	n/a
3	REST	chr5:59561608-59562010	PFSK-1	brain:	n/a	chr5:59561837-59561846
4	REST	chr5:59561714-59561985	H1-hESC	embryonic stem cell:	n/a	chr5:59561837-59561846
5	REST	chr5:59561715-59561997	SK-N-SH	brain:	n/a	chr5:59561837-59561846
6	FOXA1	chr5:59561588-59561852	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10051717	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10059334	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10064516	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10074696	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs10077172	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10471474	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12520400	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12523473	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4328990	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4404639	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4410606	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4604150	0.96[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4700370	1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[ASN][1000 genomes]
rs59518781	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60399456	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370659	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62371960	0.93[ASN][1000 genomes]
rs6862158	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72755103	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7444733	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7714765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7728100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv4847	chr5:59523591-59569307	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12516794	SLC2A4	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59554200-59562400	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr5:59558600-59563600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:59559600-59563400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr5:59559600-59563600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:59559600-59584800	Weak transcription	Primary B cells from cord blood	blood
6	chr5:59560800-59562600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:59561000-59562000	Enhancers	Gastric	stomach
8	chr5:59561600-59562000	Enhancers	HepG2	liver
9	chr5:59561600-59576600	Weak transcription	Placenta Amnion	Placenta Amnion

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