Variant report

Variant	rs41515854
Chromosome Location	chr4:82269628-82269629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10006067	0.80[AMR][1000 genomes]
rs10488936	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11723613	0.88[ASN][1000 genomes]
rs11723619	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11725731	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11732408	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11938641	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1377057	0.89[ASN][1000 genomes]
rs1452374	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1473160	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17005118	0.80[AMR][1000 genomes]
rs17427459	0.88[ASN][1000 genomes]
rs17427571	0.95[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17499327	0.88[ASN][1000 genomes]
rs17499732	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17499829	0.86[EUR][1000 genomes]
rs17499843	0.86[EUR][1000 genomes]
rs1878528	0.85[EUR][1000 genomes]
rs1975474	0.81[EUR][1000 genomes]
rs2011962	0.89[ASN][1000 genomes]
rs2034629	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2034632	0.88[ASN][1000 genomes]
rs2058368	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2109662	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2839753	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34347934	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41501452	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56075827	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57222629	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58877260	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59498284	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60825648	0.88[ASN][1000 genomes]
rs61371439	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62302352	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62303570	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6535240	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6812825	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6813437	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6824784	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs710835	1.00[JPT][hapmap]
rs725826	0.95[ASN][1000 genomes]
rs7656390	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7658313	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7669368	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7685840	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7696324	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7698086	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7698361	0.83[EUR][1000 genomes]
rs7699396	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7699600	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs788855	1.00[JPT][hapmap]
rs788861	1.00[JPT][hapmap]

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	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829985	chr4:82199328-82353656	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41515854	PAQR3	cis	cerebellum	SCAN
rs41515854	COPS4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82267600-82273400	Enhancers	Fetal Intestine Large	intestine
2	chr4:82268000-82270600	Enhancers	Fetal Intestine Small	intestine
3	chr4:82269600-82270200	Enhancers	Fetal Lung	lung

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