Variant report

Variant	rs864354
Chromosome Location	chr5:142634708-142634709
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10041520	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs10052957	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs11750560	0.83[EUR][1000 genomes]
rs1866388	0.80[LWK][hapmap];0.81[YRI][hapmap]
rs190488	0.85[YRI][hapmap]
rs258747	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs258750	0.88[ASW][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap]
rs258763	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs258813	0.81[ASW][hapmap];0.84[LWK][hapmap]
rs2918416	0.88[ASW][hapmap];0.89[LWK][hapmap];0.92[YRI][hapmap]
rs2918417	0.82[ASW][hapmap];0.89[LWK][hapmap];0.85[YRI][hapmap]
rs2963149	0.88[ASW][hapmap];0.88[LWK][hapmap];0.92[YRI][hapmap]
rs33383	0.86[GIH][hapmap];0.93[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs33388	0.92[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs4634384	0.95[CEU][hapmap];0.82[JPT][hapmap]
rs6188	0.88[ASW][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap]
rs6191	0.83[EUR][1000 genomes]
rs6877893	0.88[CEU][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs852976	0.80[EUR][1000 genomes]
rs852977	0.88[ASW][hapmap];0.84[LWK][hapmap];0.92[YRI][hapmap]
rs852980	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs852982	0.85[YRI][hapmap]
rs853175	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs853180	0.84[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap]
rs853183	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs860457	0.85[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	esv1825941	chr5:142568715-142728031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs864354	PCDHB16	cis	cerebellum	SCAN
rs864354	SRA1	cis	cerebellum	SCAN
rs864354	NR3C1	Cis_1M	lymphoblastoid	RTeQTL
rs864354	LARS	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142629600-142641600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:142629800-142640800	Weak transcription	NHLF	lung
3	chr5:142630000-142636800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:142630000-142641000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:142630200-142638200	Weak transcription	NHEK	skin
6	chr5:142632200-142636800	Weak transcription	K562	blood

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