Variant report

Variant	rs505382
Chromosome Location	chr5:112194144-112194145
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112191204..112194360-chr5:112195263..112198616,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153037	Chromatin interaction
ENSG00000272869	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1093611	0.87[ASN][1000 genomes]
rs149193	0.84[EUR][1000 genomes]
rs153544	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs153546	0.85[ASN][1000 genomes]
rs153548	0.85[ASN][1000 genomes]
rs153549	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs153550	0.85[ASN][1000 genomes]
rs153551	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs153552	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs154344	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2545155	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2545156	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2545170	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2546112	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3317	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs351767	0.90[ASN][1000 genomes]
rs351768	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351770	0.92[ASN][1000 genomes]
rs368575	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs373059	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs374613	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382427	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs395858	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs410701	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41116	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs419155	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs448162	0.94[ASN][1000 genomes]
rs448475	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs448613	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs454968	0.95[ASN][1000 genomes]
rs456531	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs459102	0.87[ASN][1000 genomes]
rs460137	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs468751	0.84[EUR][1000 genomes]
rs468854	0.81[ASN][1000 genomes]
rs469827	0.84[ASN][1000 genomes]
rs469886	0.84[EUR][1000 genomes]
rs495794	0.90[ASN][1000 genomes]
rs514763	0.88[ASN][1000 genomes]
rs566419	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67293732	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs712663	0.86[ASN][1000 genomes]
rs712670	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7213	0.90[ASN][1000 genomes]
rs818426	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs818428	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs818429	0.87[ASN][1000 genomes]
rs818430	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs818797	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1034239	chr5:112161239-112194693	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS 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	19 gene(s)	inside rSNPs	diseases
5	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs505382	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs505382	REEP5	cis	Esophagus Muscularis	GTEx
rs505382	REEP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112189400-112196200	Weak transcription	Spleen	Spleen
2	chr5:112191400-112196400	Weak transcription	HepG2	liver
3	chr5:112192400-112196400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:112193600-112196000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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