Variant report

Variant	rs62571027
Chromosome Location	chr9:15515899-15515900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:15497676..15499594-chr9:15514470..15516149,2	MCF-7	breast:
2	chr9:15510264..15513012-chr9:15513420..15518300,5	K562	blood:
3	chr9:15509655..15511884-chr9:15514283..15517212,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10124624	0.88[ASN][1000 genomes]
rs10283923	0.85[ASN][1000 genomes]
rs10283927	0.85[ASN][1000 genomes]
rs12336503	0.85[ASN][1000 genomes]
rs12336509	0.85[ASN][1000 genomes]
rs12339417	0.85[ASN][1000 genomes]
rs12683553	0.85[ASN][1000 genomes]
rs16933311	0.85[ASN][1000 genomes]
rs16933320	0.81[ASN][1000 genomes]
rs16933348	0.94[ASN][1000 genomes]
rs16933350	0.80[EUR][1000 genomes]
rs1828382	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1828383	0.88[ASN][1000 genomes]
rs2175257	0.85[ASN][1000 genomes]
rs2277191	0.84[ASN][1000 genomes]
rs2777950	0.84[ASN][1000 genomes]
rs28537229	0.83[ASN][1000 genomes]
rs55771541	0.90[ASN][1000 genomes]
rs56361298	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57142629	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57191285	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57467578	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57849124	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58607272	0.88[ASN][1000 genomes]
rs58915725	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59520337	0.80[EUR][1000 genomes]
rs59639757	0.90[ASN][1000 genomes]
rs62571010	0.85[ASN][1000 genomes]
rs62571018	0.80[EUR][1000 genomes]
rs62571021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62571023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62571024	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62571029	0.80[EUR][1000 genomes]
rs62571030	0.90[ASN][1000 genomes]
rs62571031	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62571032	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6474927	0.90[ASN][1000 genomes]
rs7018658	0.85[ASN][1000 genomes]
rs7021153	0.81[ASN][1000 genomes]
rs7023730	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73408328	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73408340	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73644657	0.90[ASN][1000 genomes]
rs7852774	0.88[ASN][1000 genomes]
rs7856710	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7857933	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7863139	0.91[EUR][1000 genomes];0.85[ASN][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	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62571027	PSIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15513400-15521800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:15513600-15516600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:15513600-15521400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:15513800-15521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:15514600-15521200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:15515800-15516000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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