Variant report

Variant	rs285559
Chromosome Location	chr12:41929813-41929814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10506188	1.00[JPT][hapmap]
rs10748302	1.00[JPT][hapmap]
rs10785269	1.00[JPT][hapmap]
rs10880081	1.00[JPT][hapmap]
rs10880082	1.00[JPT][hapmap]
rs10880087	1.00[JPT][hapmap]
rs10880088	1.00[JPT][hapmap]
rs11180936	1.00[JPT][hapmap]
rs11180943	1.00[JPT][hapmap]
rs11180961	0.85[JPT][hapmap]
rs12299762	0.83[GIH][hapmap]
rs12322329	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs12372586	1.00[JPT][hapmap]
rs12423463	1.00[MEX][hapmap]
rs12424813	1.00[MEX][hapmap]
rs169564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17579291	1.00[JPT][hapmap]
rs2254521	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs2446145	0.82[EUR][1000 genomes]
rs2468312	0.99[EUR][1000 genomes]
rs2599254	1.00[CEU][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608698	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2608699	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2608709	1.00[JPT][hapmap]
rs2608713	0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2608717	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2730812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730815	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2730825	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2730831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733288	0.88[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs285551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285552	0.97[EUR][1000 genomes]
rs285553	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs285554	0.99[EUR][1000 genomes]
rs285558	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs285570	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs285571	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs285572	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs285573	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs285576	0.91[EUR][1000 genomes]
rs285584	0.88[AMR][1000 genomes]
rs285588	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285589	0.82[EUR][1000 genomes]
rs285591	0.87[GIH][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs285594	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110189	1.00[JPT][hapmap]
rs392217	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768355	1.00[JPT][hapmap]
rs61548934	0.97[ASN][1000 genomes]
rs7133340	0.83[GIH][hapmap]
rs74077823	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	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv899040	chr12:41905897-42181706	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs285559	PDZRN4	cis	brain	seeQTL
rs285559	PDZRN4	cis	parietal	SCAN
rs285559	KIF21A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41925600-41949800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:41925800-41944800	Weak transcription	Brain Germinal Matrix	brain
3	chr12:41929400-41933000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:41929800-41930000	Enhancers	Fetal Lung	lung

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