Variant report

Variant	rs4041
Chromosome Location	chr5:114521710-114521711
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10055468	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057172	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059320	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061960	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070542	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077453	1.00[JPT][hapmap];0.96[MKK][hapmap]
rs10078804	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017208	1.00[JPT][hapmap]
rs11950355	1.00[JPT][hapmap]
rs17459144	0.91[JPT][hapmap]
rs2305130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267304	0.81[MKK][hapmap]
rs2909843	1.00[JPT][hapmap]
rs2963769	1.00[JPT][hapmap]
rs2963770	0.91[JPT][hapmap]
rs2963771	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2963773	1.00[JPT][hapmap]
rs2963774	0.91[JPT][hapmap]
rs2964543	1.00[JPT][hapmap]
rs2964544	1.00[JPT][hapmap]
rs4596375	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705732	1.00[JPT][hapmap]
rs7734074	1.00[JPT][hapmap]
rs9326953	1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830453	chr5:114277261-114546536	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv462399	chr5:114445023-114526010	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv599477	chr5:114445023-114526010	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4041	PGGT1B	cis	uninvolved skin	skin_eQTL
rs4041	PGGT1B	cis	lesional skin	skin_eQTL
rs4041	CCDC112	cis	parietal	SCAN
rs4041	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs4041	PGGT1B	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114518400-114525400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:114520600-114521800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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