Variant report

Variant	rs621806
Chromosome Location	chr4:20553304-20553305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10031950	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11936468	0.93[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2446087	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs532992	0.81[CEU][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576127	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603679	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs609535	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];0.93[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs649424	1.00[JPT][hapmap]
rs652756	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819634	1.00[JPT][hapmap]
rs7666974	0.89[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9291411	0.83[EUR][1000 genomes]
rs9992591	0.95[GIH][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs9992598	1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
2	nsv999482	chr4:20546216-20563747	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1007227	chr4:20547578-20563930	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv516999	chr4:20548976-20565861	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3692811	chr4:20552510-20565861	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs621806	PACRGL	cis	cerebellum	SCAN

Chromatin state (count:36 , 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	chr4:20524200-20555200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:20525200-20555400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:20530400-20555400	Weak transcription	NHEK	skin
7	chr4:20533000-20578000	Weak transcription	NHLF	lung
8	chr4:20533800-20576200	Weak transcription	Left Ventricle	heart
9	chr4:20534800-20576400	Weak transcription	Fetal Brain Male	brain
10	chr4:20535800-20593600	Weak transcription	Fetal Kidney	kidney
11	chr4:20536000-20554800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:20536000-20555200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:20536600-20572200	Weak transcription	Placenta	Placenta
14	chr4:20536800-20618600	Weak transcription	Spleen	Spleen
15	chr4:20547000-20576000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:20549200-20568800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:20550000-20561400	Strong transcription	NHDF-Ad	bronchial
18	chr4:20550400-20561000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:20550800-20553400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:20552000-20554800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:20552000-20557600	Strong transcription	Fetal Lung	lung
22	chr4:20552400-20553400	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr4:20552400-20555400	Strong transcription	Osteobl	bone
24	chr4:20552400-20561000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:20552600-20553600	Strong transcription	Colon Smooth Muscle	Colon
26	chr4:20552600-20553800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:20552600-20556000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:20552600-20558600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:20552800-20553400	Strong transcription	Brain Anterior Caudate	brain
30	chr4:20552800-20553800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:20552800-20555600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:20552800-20556000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:20553000-20569200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:20553200-20553600	Weak transcription	Lung	lung
35	chr4:20553200-20554200	Strong transcription	Fetal Stomach	stomach
36	chr4:20553200-20555400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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