Variant report

Variant	rs1545823
Chromosome Location	chr4:86464117-86464118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10017712	0.89[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10020489	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029756	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10029852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10032314	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097059	0.84[MEX][hapmap]
rs11723931	0.80[ASN][1000 genomes]
rs11728289	0.80[ASN][1000 genomes]
rs11946933	0.83[ASN][1000 genomes]
rs12108232	0.81[ASN][1000 genomes]
rs12500479	0.91[ASN][1000 genomes]
rs12501745	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs12506039	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510597	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs12510645	0.92[ASN][1000 genomes]
rs12644974	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13139321	0.92[ASN][1000 genomes]
rs13140816	0.92[ASN][1000 genomes]
rs1548107	0.81[ASN][1000 genomes]
rs17387199	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17387344	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1871824	0.90[ASN][1000 genomes]
rs1871825	0.90[ASN][1000 genomes]
rs1994065	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1994068	0.81[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2062080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2128092	0.81[ASN][1000 genomes]
rs2128100	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs2170418	0.80[ASN][1000 genomes]
rs2869352	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]
rs2869355	0.83[ASN][1000 genomes]
rs34662286	0.81[ASN][1000 genomes]
rs4693703	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4693704	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838692	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6839494	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7657835	0.94[ASN][1000 genomes]
rs964837	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9994597	0.83[ASN][1000 genomes]
rs9994823	0.92[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1545823	SNCA	cis	cerebellum	SCAN
rs1545823	TIGD2	cis	cerebellum	SCAN
rs1545823	ARHGAP24	cis	lymphoblastoid	seeQTL
rs1545823	ARHGAP24	Cis_1M	lymphoblastoid	RTeQTL

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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