Variant report

Variant	rs609535
Chromosome Location	chr4:20568566-20568567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10031950	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11936468	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2446087	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs532992	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603679	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs621806	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636798	0.89[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs649424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs652756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819634	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7666974	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9291411	0.86[EUR][1000 genomes]
rs9992591	0.97[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9992598	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829875	chr4:20502895-20680956	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs609535	PACRGL	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20492000-20599800	Weak transcription	Aorta	Aorta
2	chr4:20511800-20576200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:20519400-20571000	Weak transcription	Adipose Nuclei	Adipose
4	chr4:20533000-20578000	Weak transcription	NHLF	lung
5	chr4:20533800-20576200	Weak transcription	Left Ventricle	heart
6	chr4:20534800-20576400	Weak transcription	Fetal Brain Male	brain
7	chr4:20535800-20593600	Weak transcription	Fetal Kidney	kidney
8	chr4:20536600-20572200	Weak transcription	Placenta	Placenta
9	chr4:20536800-20618600	Weak transcription	Spleen	Spleen
10	chr4:20547000-20576000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:20549200-20568800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:20553000-20569200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:20554200-20576600	Weak transcription	Fetal Stomach	stomach
14	chr4:20555200-20585600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:20555400-20569200	Weak transcription	Osteobl	bone
16	chr4:20555600-20599200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:20556000-20591000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:20560000-20583200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:20561000-20568600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:20566000-20569000	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:20567000-20574200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:20567000-20581800	Weak transcription	NHEK	skin
23	chr4:20567000-20604000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:20567200-20605200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:20567200-20617000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:20567400-20572800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:20567600-20572400	Strong transcription	Fetal Lung	lung
28	chr4:20567800-20574800	Strong transcription	NHDF-Ad	bronchial
29	chr4:20568200-20569600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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