Variant report

Variant	rs12351630
Chromosome Location	chr9:116068552-116068553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116064327..116066075-chr9:116067719..116071203,3	MCF-7	breast:
2	chr9:116068063..116070072-chr9:116225763..116227656,2	MCF-7	breast:
3	chr9:116056474..116058317-chr9:116067548..116069839,2	K562	blood:
4	chr9:116068239..116070626-chr9:116128043..116129865,2	MCF-7	breast:
5	chr9:115981707..115983600-chr9:116067102..116069964,2	MCF-7	breast:
6	chr9:116068116..116070060-chr9:116164564..116167189,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165188	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000138835	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10481639	0.93[EUR][1000 genomes]
rs10817480	0.93[EUR][1000 genomes]
rs10981726	0.98[EUR][1000 genomes]
rs10981731	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10981733	0.97[EUR][1000 genomes]
rs10981740	0.93[EUR][1000 genomes]
rs10981741	0.93[EUR][1000 genomes]
rs10981742	0.93[EUR][1000 genomes]
rs10981743	0.93[EUR][1000 genomes]
rs10981744	0.93[EUR][1000 genomes]
rs10981745	0.93[EUR][1000 genomes]
rs10981746	0.93[EUR][1000 genomes]
rs10981747	0.93[EUR][1000 genomes]
rs10981748	0.93[EUR][1000 genomes]
rs10981750	0.92[EUR][1000 genomes]
rs10981751	0.93[EUR][1000 genomes]
rs10981752	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10981760	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12006029	0.93[EUR][1000 genomes]
rs12336832	0.87[ASN][1000 genomes]
rs12337552	0.97[EUR][1000 genomes]
rs12338029	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12339382	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12341669	0.95[ASN][1000 genomes]
rs12342197	0.95[ASN][1000 genomes]
rs12342549	0.95[ASN][1000 genomes]
rs12343330	0.87[ASN][1000 genomes]
rs12344170	0.93[EUR][1000 genomes]
rs12344525	0.93[EUR][1000 genomes]
rs12348629	0.95[ASN][1000 genomes]
rs12349495	0.87[ASN][1000 genomes]
rs12349500	0.95[ASN][1000 genomes]
rs12349614	0.87[ASN][1000 genomes]
rs12351134	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12351168	0.95[ASN][1000 genomes]
rs12351296	0.93[EUR][1000 genomes]
rs12352784	0.91[ASN][1000 genomes]
rs12352925	0.86[ASN][1000 genomes]
rs13440199	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1543535	0.93[EUR][1000 genomes]
rs16932583	0.97[EUR][1000 genomes]
rs16932649	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17764563	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17831256	0.91[ASN][1000 genomes]
rs28495580	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28607343	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28733164	0.95[ASN][1000 genomes]
rs41276795	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4324980	0.93[EUR][1000 genomes]
rs4437724	0.93[EUR][1000 genomes]
rs4442214	0.87[EUR][1000 genomes]
rs4445296	0.93[EUR][1000 genomes]
rs4560870	0.92[EUR][1000 genomes]
rs4636275	0.93[EUR][1000 genomes]
rs5012573	0.97[EUR][1000 genomes]
rs58402825	0.87[ASN][1000 genomes]
rs60528957	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66509679	0.87[ASN][1000 genomes]
rs66649870	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67292897	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7025347	0.93[EUR][1000 genomes]
rs7027445	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7041782	0.93[EUR][1000 genomes]
rs7863485	0.93[EUR][1000 genomes]
rs7863910	1.00[ASN][1000 genomes]
rs7865438	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7875945	0.97[EUR][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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12351630	BSPRY	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116055200-116085200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
3	chr9:116062600-116075600	Weak transcription	Placenta	Placenta
4	chr9:116065400-116086800	Weak transcription	Gastric	stomach
5	chr9:116065600-116079000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:116065600-116083400	Weak transcription	Esophagus	oesophagus
7	chr9:116065800-116069800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:116066000-116069800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:116068400-116070200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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