Variant report

Variant	rs620102
Chromosome Location	chr6:150692480-150692481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12193715	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12198459	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200125	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203809	1.00[ASN][1000 genomes]
rs12211677	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211918	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211979	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1768283	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55977741	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632750	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654476	0.87[CEU][hapmap]
rs655363	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs657961	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs660467	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667815	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs674414	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678182	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683150	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs683620	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73001817	0.87[ASN][1000 genomes]
rs9397289	1.00[CHB][hapmap]
rs9478711	1.00[ASN][1000 genomes]
rs9480324	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480328	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480329	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[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	esv2763602	chr6:150581193-150720666	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3393784	chr6:150689259-150693557	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs620102	LRP11	cis	cerebellum	SCAN
rs620102	PPP1R14C	cis	parietal	SCAN
rs620102	NOX4	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150689200-150693200	Enhancers	Fetal Intestine Large	intestine
2	chr6:150689200-150693400	Enhancers	Fetal Intestine Small	intestine
3	chr6:150691000-150698200	Weak transcription	Stomach Mucosa	stomach
4	chr6:150691600-150700200	Weak transcription	Lung	lung
5	chr6:150691800-150695000	Enhancers	Liver	Liver
6	chr6:150692200-150694600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:150692200-150698200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:150692400-150695200	Enhancers	Muscle Satellite Cultured Cells	--

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