Variant report

Variant	rs59520337
Chromosome Location	chr9:15515759-15515760
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: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs16933296	0.90[EUR][1000 genomes]
rs16933350	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3087653	0.95[EUR][1000 genomes]
rs41268961	0.95[EUR][1000 genomes]
rs41306098	0.95[EUR][1000 genomes]
rs56361298	0.80[EUR][1000 genomes]
rs57191285	0.80[EUR][1000 genomes]
rs57467578	0.80[EUR][1000 genomes]
rs57849124	0.80[EUR][1000 genomes]
rs58168894	0.85[AFR][1000 genomes]
rs59355275	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62570969	0.81[EUR][1000 genomes]
rs62570970	0.85[EUR][1000 genomes]
rs62570971	0.85[EUR][1000 genomes]
rs62570972	0.81[EUR][1000 genomes]
rs62570973	0.85[EUR][1000 genomes]
rs62570974	0.85[EUR][1000 genomes]
rs62570975	0.85[EUR][1000 genomes]
rs62570976	0.90[EUR][1000 genomes]
rs62570980	0.95[EUR][1000 genomes]
rs62570991	0.95[EUR][1000 genomes]
rs62570992	0.95[EUR][1000 genomes]
rs62570993	0.95[EUR][1000 genomes]
rs62571001	0.90[EUR][1000 genomes]
rs62571002	0.90[EUR][1000 genomes]
rs62571003	0.92[EUR][1000 genomes]
rs62571007	0.95[EUR][1000 genomes]
rs62571008	0.92[EUR][1000 genomes]
rs62571009	0.95[EUR][1000 genomes]
rs62571011	0.95[EUR][1000 genomes]
rs62571015	0.95[EUR][1000 genomes]
rs62571016	0.95[EUR][1000 genomes]
rs62571017	0.95[EUR][1000 genomes]
rs62571018	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571021	0.80[EUR][1000 genomes]
rs62571022	0.80[EUR][1000 genomes]
rs62571023	0.80[EUR][1000 genomes]
rs62571024	0.80[EUR][1000 genomes]
rs62571027	0.80[EUR][1000 genomes]
rs62571029	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571033	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571037	0.92[EUR][1000 genomes]
rs62571046	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62571047	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62571048	0.90[EUR][1000 genomes]
rs62571050	0.87[EUR][1000 genomes]
rs62571051	0.85[EUR][1000 genomes]
rs62571052	0.82[EUR][1000 genomes]
rs73408328	0.80[EUR][1000 genomes]
rs73408340	0.80[EUR][1000 genomes]
rs73410204	0.90[AFR][1000 genomes]
rs73410215	0.85[AFR][1000 genomes]
rs7856523	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7856657	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7856710	0.85[AFR][1000 genomes]
rs7863139	0.80[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	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
rs59520337	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	chr9:15513800-15515800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:15513800-15521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:15514600-15521200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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