Variant report

Variant	rs8099016
Chromosome Location	chr18:11696064-11696065
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1013459	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs11872939	1.00[CHD][hapmap]
rs1477484	1.00[CHD][hapmap]
rs16976596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16976628	1.00[CHD][hapmap]
rs17515304	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17515325	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1863122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035194	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035195	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28620345	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4239300	1.00[JPT][hapmap]
rs57892223	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61124787	0.84[ASN][1000 genomes]
rs61670374	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505670	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71367576	0.92[ASN][1000 genomes]
rs7236433	0.84[ASN][1000 genomes]
rs7237466	0.85[ASN][1000 genomes]
rs7237945	0.85[ASN][1000 genomes]
rs72881064	0.84[ASN][1000 genomes]
rs8085488	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8087266	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8087897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8090096	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8090294	0.83[ASW][hapmap]
rs8096345	0.88[ASW][hapmap];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[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8098596	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099153	1.00[CHD][hapmap]
rs8099179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099342	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099486	0.92[ASN][1000 genomes]
rs9303742	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9303743	1.00[CHD][hapmap]
rs9675415	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9676233	1.00[CHD][hapmap]
rs9946455	1.00[CHD][hapmap]
rs9966615	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066659	chr18:11246502-11709409	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8099016	MPPE1	cis	lesional skin	skin_eQTL
rs8099016	GNAL	cis	multi-tissue	Pritchard
rs8099016	AFG3L2	cis	parietal	SCAN
rs8099016	MPPE1	cis	normal skin	skin_eQTL
rs8099016	MPPE1	cis	uninvolved skin	skin_eQTL
rs8099016	GNAL	cis	lesional skin	skin_eQTL
rs8099016	TUBB6	cis	parietal	SCAN
rs8099016	GNAL	cis	uninvolved skin	skin_eQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11690400-11713800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:11694400-11697400	Enhancers	NHEK	skin
3	chr18:11695000-11696200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr18:11695200-11696200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr18:11695200-11696400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr18:11695200-11696400	Enhancers	HMEC	breast
7	chr18:11695800-11696800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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