Variant report

Variant	rs6580523
Chromosome Location	chr5:147499426-147499427
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10059165	0.96[AFR][1000 genomes]
rs10060151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065596	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10515602	0.83[CHB][hapmap]
rs10515603	0.83[CHB][hapmap]
rs11168033	0.89[CHB][hapmap]
rs11743440	0.83[CHB][hapmap]
rs11948406	0.82[CHB][hapmap]
rs12187820	0.83[CHB][hapmap]
rs12188819	0.83[CHB][hapmap]
rs1422987	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17704908	0.83[CHB][hapmap]
rs2052531	0.83[CHB][hapmap]
rs2052532	0.83[CHB][hapmap]
rs2052534	0.86[CHB][hapmap]
rs2052536	0.85[CHB][hapmap]
rs2112765	0.91[CHB][hapmap]
rs2112766	0.86[CHB][hapmap]
rs2112767	0.83[CHB][hapmap]
rs2161434	0.86[CHB][hapmap]
rs2303064	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303074	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303075	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756690	0.83[CHB][hapmap]
rs3764930	0.83[CHB][hapmap]
rs3764931	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777134	0.83[CHB][hapmap]
rs3777135	0.83[CHB][hapmap]
rs4349706	0.83[CHB][hapmap]
rs4705054	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6873836	0.83[CHB][hapmap]
rs6895434	0.90[CHB][hapmap]
rs7725816	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs9325071	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325072	0.96[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580523	PPP2R2B	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147470400-147518400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr5:147470600-147508400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:147470600-147509000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:147471600-147514800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:147472000-147505000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:147474200-147513400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:147479000-147500600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:147481400-147513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:147481600-147505000	Weak transcription	Esophagus	oesophagus
10	chr5:147482200-147509000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:147486800-147515000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:147487400-147505000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:147487800-147525800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:147494000-147500400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:147495000-147500200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:147496200-147501600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:147497200-147500400	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr5:147497200-147501200	Weak transcription	Hela-S3	cervix
19	chr5:147497800-147500200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:147498800-147513000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:147499200-147500200	Enhancers	Brain Cingulate Gyrus	brain
22	chr5:147499400-147499600	Enhancers	Brain Hippocampus Middle	brain

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