Variant report

Variant	rs6864442
Chromosome Location	chr5:59710033-59710034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10056638	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10073390	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11745274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159422	0.88[ASW][hapmap];0.81[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs1345782	0.88[JPT][hapmap]
rs1423471	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs1423473	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs16877964	0.88[JPT][hapmap]
rs16877967	0.88[JPT][hapmap]
rs16877993	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs16878035	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16878037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16878086	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs16878106	1.00[CHB][hapmap]
rs16878108	0.92[CHB][hapmap]
rs17326404	0.88[JPT][hapmap]
rs17378750	0.88[JPT][hapmap]
rs1862589	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs28460011	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28635931	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3763059	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs37691	0.83[ASW][hapmap];0.92[YRI][hapmap]
rs37695	0.80[AFR][1000 genomes]
rs4090603	0.91[CHB][hapmap]
rs446883	0.89[YRI][hapmap]
rs56151644	0.97[ASN][1000 genomes]
rs58376959	0.97[ASN][1000 genomes]
rs6449471	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs6860277	0.83[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs6875484	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6878429	0.92[CHB][hapmap]
rs6886304	0.88[JPT][hapmap]
rs6887545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891858	0.92[CHB][hapmap]
rs6896850	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73759052	0.97[ASN][1000 genomes]
rs73759053	0.97[ASN][1000 genomes]
rs73759054	0.97[ASN][1000 genomes]
rs7702188	0.88[JPT][hapmap]
rs7702474	0.91[CHB][hapmap]
rs7705194	0.92[CHB][hapmap]
rs7712662	0.91[CHB][hapmap]
rs7723861	0.92[CHB][hapmap]
rs7725629	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs7734108	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs789389	0.83[ASW][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs9291690	1.00[AFR][1000 genomes];0.99[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	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	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1015381	chr5:59678425-59772485	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1034331	chr5:59678773-59773467	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1033344	chr5:59710033-59773467	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6864442	PDE4D	cis	cerebellum	SCAN
rs6864442	ARHGAP44	trans	cerebellum	SCAN
rs6864442	PLK2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59695000-59712600	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59696000-59713200	Weak transcription	Aorta	Aorta
3	chr5:59707200-59712400	Weak transcription	HepG2	liver

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