Variant report

Variant	rs1564760
Chromosome Location	chr3:47582724-47582725
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1038394	0.90[YRI][hapmap]
rs10865946	0.90[YRI][hapmap]
rs11130133	0.87[ASN][1000 genomes]
rs11130137	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs11705957	0.81[GIH][hapmap]
rs11707895	0.93[ASN][1000 genomes]
rs11711265	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.91[ASN][1000 genomes]
rs11711824	0.85[YRI][hapmap]
rs11712445	0.90[YRI][hapmap]
rs11713413	0.84[ASN][1000 genomes]
rs11719877	0.81[GIH][hapmap];0.90[YRI][hapmap]
rs11914932	0.89[ASN][1000 genomes]
rs13059519	0.81[GIH][hapmap];0.90[YRI][hapmap]
rs13075233	0.81[GIH][hapmap];0.90[YRI][hapmap]
rs1531875	0.90[YRI][hapmap]
rs1564761	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17784882	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1872164	0.81[GIH][hapmap]
rs1872166	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291298	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs295458	0.85[YRI][hapmap]
rs34634681	0.93[ASN][1000 genomes]
rs3816779	0.81[GIH][hapmap];0.90[YRI][hapmap]
rs4599332	0.86[ASN][1000 genomes]
rs4858856	0.91[ASN][1000 genomes]
rs4858868	0.90[YRI][hapmap]
rs4858894	0.90[YRI][hapmap]
rs62260710	0.91[ASN][1000 genomes]
rs62260711	0.91[ASN][1000 genomes]
rs62260741	0.92[ASN][1000 genomes]
rs6768879	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6790763	0.92[ASN][1000 genomes]
rs7628631	0.91[ASN][1000 genomes]
rs878659	0.90[YRI][hapmap]
rs9683033	0.90[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1564760	C3orf75	cis	cerebellum	SCAN
rs1564760	SCAP	cis	parietal	SCAN
rs1564760	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs1564760	SETD2	cis	cerebellum	SCAN
rs1564760	PRKAR2A	cis	cerebellum	SCAN
rs1564760	HYAL2	cis	cerebellum	SCAN
rs1564760	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47577000-47583000	Weak transcription	K562	blood
2	chr3:47578600-47583800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:47578800-47586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47579200-47583000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:47579200-47583200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:47582000-47583800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:47582200-47583600	Bivalent Enhancer	HepG2	liver
8	chr3:47582400-47584000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:47582400-47584200	Weak transcription	Esophagus	oesophagus
10	chr3:47582600-47582800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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