Variant report

Variant	rs11097059
Chromosome Location	chr4:86463980-86463981
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10000472	0.83[MEX][hapmap]
rs10017712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10029756	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10029852	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs11930449	0.87[MEX][hapmap]
rs11945598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11946933	0.82[ASN][1000 genomes]
rs12108232	0.80[ASN][1000 genomes]
rs12504294	0.83[MEX][hapmap]
rs12510597	0.82[CHD][hapmap]
rs12644260	0.83[MEX][hapmap]
rs13139830	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1384132	0.83[MEX][hapmap]
rs1384137	0.87[MEX][hapmap]
rs1545823	0.84[MEX][hapmap]
rs1548107	0.80[ASN][1000 genomes]
rs2128092	0.80[ASN][1000 genomes]
rs2128100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28481407	0.83[MEX][hapmap]
rs2869355	0.82[ASN][1000 genomes]
rs34662286	0.80[ASN][1000 genomes]
rs34683578	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35904519	0.90[ASN][1000 genomes]
rs4693122	0.83[MEX][hapmap]
rs4693702	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58607125	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62315600	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964837	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9884932	0.83[MEX][hapmap]
rs9994597	0.82[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	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11097059	AFF1	cis	parietal	SCAN
rs11097059	PKD2	cis	cerebellum	SCAN
rs11097059	ARHGAP24	Cis_1M	lymphoblastoid	RTeQTL
rs11097059	ARHGAP24	cis	lymphoblastoid	seeQTL
rs11097059	SNCA	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86430200-86468600	Weak transcription	Pancreas	Pancrea
2	chr4:86445400-86464600	Weak transcription	HSMM	muscle
3	chr4:86452200-86465000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:86454000-86476600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:86454600-86471800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:86454800-86471800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:86456000-86464200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr4:86457800-86470400	Weak transcription	Primary B cells from cord blood	blood
9	chr4:86458200-86466600	Weak transcription	Right Atrium	heart
10	chr4:86461000-86476600	Weak transcription	Left Ventricle	heart
11	chr4:86462400-86464400	Weak transcription	Gastric	stomach
12	chr4:86463800-86464800	Enhancers	Fetal Heart	heart

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