Variant report

Variant	rs1539871
Chromosome Location	chr18:45467806-45467807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:45455692..45459621-chr18:45464171..45467892,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10502890	0.81[ASW][hapmap];0.89[LWK][hapmap]
rs11082638	0.86[GIH][hapmap];0.83[MEX][hapmap]
rs12457664	0.81[ASW][hapmap];0.89[LWK][hapmap]
rs12968493	0.89[LWK][hapmap]
rs12969725	0.81[ASW][hapmap];0.89[LWK][hapmap]
rs1539872	0.91[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs1573363	0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1631576	0.83[GIH][hapmap]
rs1787185	0.90[JPT][hapmap]
rs1787186	0.86[LWK][hapmap]
rs1787193	0.90[JPT][hapmap]
rs1787194	0.90[JPT][hapmap]
rs1787196	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1792655	0.90[JPT][hapmap]
rs1792658	0.89[LWK][hapmap];0.87[YRI][hapmap]
rs1792668	0.89[LWK][hapmap]
rs1792670	0.89[GIH][hapmap];0.95[MEX][hapmap]
rs1792671	0.90[JPT][hapmap]
rs1792674	0.81[ASW][hapmap];0.89[LWK][hapmap]
rs1792675	0.90[JPT][hapmap]
rs1792679	0.90[JPT][hapmap]
rs1792681	0.89[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap]
rs1792682	0.90[JPT][hapmap]
rs1792683	0.83[GIH][hapmap]
rs1792684	0.92[LWK][hapmap]
rs1792686	0.87[ASW][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap]
rs1792687	0.87[LWK][hapmap]
rs1981	0.92[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs2000708	0.83[JPT][hapmap]
rs2000709	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2012555	0.94[ASW][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3813068	0.91[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs4940109	0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap]
rs4940110	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4940120	0.92[ASN][1000 genomes]
rs4940127	0.92[ASN][1000 genomes]
rs61513611	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6507790	0.89[GIH][hapmap];0.84[MEX][hapmap]
rs7228393	0.89[GIH][hapmap];0.80[MEX][hapmap]
rs7236177	0.89[GIH][hapmap];0.85[MEX][hapmap]
rs729112	0.89[GIH][hapmap];0.85[MEX][hapmap]
rs765213	0.83[JPT][hapmap]
rs8095519	0.89[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap]
rs8097912	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs948604	0.89[GIH][hapmap];0.85[MEX][hapmap]
rs9946556	0.90[JPT][hapmap]
rs9955626	0.83[AMR][1000 genomes]
rs9966964	0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909614	chr18:45419421-45478490	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv909615	chr18:45452321-45493026	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv909616	chr18:45467806-45844500	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1539871	PSTPIP2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45459600-45471600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:45463800-45468400	Weak transcription	Hela-S3	cervix
3	chr18:45465200-45468200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:45465200-45468400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:45465800-45468600	Weak transcription	Dnd41	blood

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