Variant report

Variant	rs2220309
Chromosome Location	chr5:2014366-2014367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10475125	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10475127	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13153217	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs13162781	0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs13190594	0.82[CHB][hapmap];0.95[ASN][1000 genomes]
rs16902321	0.87[CHB][hapmap]
rs2129471	0.83[CHB][hapmap]
rs4975794	0.83[CHB][hapmap]
rs4975796	0.83[CHB][hapmap]
rs4975798	0.83[CHB][hapmap]
rs730633	0.91[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7729761	0.83[CHB][hapmap]
rs901499	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

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	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2220309	PPP1R2P3	trans	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:2009400-2014400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:2012600-2015200	Enhancers	Fetal Heart	heart
3	chr5:2012800-2015200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:2013200-2014600	Weak transcription	Right Ventricle	heart
5	chr5:2013200-2014800	Enhancers	HMEC	breast
6	chr5:2013200-2015600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:2013800-2018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:2014000-2015200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:2014000-2020200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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