Variant report

Variant	rs580237
Chromosome Location	chr5:112194032-112194033
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYA	chr5:112193917-112194115	GM12878	blood:	n/a	n/a

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
SRP19	TF binding region
ENSG00000272869	TF binding region
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1069061	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1093611	0.82[EUR][1000 genomes]
rs1093677	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12656359	0.83[ASN][1000 genomes]
rs151976	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs151977	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs151978	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153545	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153546	0.82[EUR][1000 genomes]
rs193527	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1966477	0.83[ASN][1000 genomes]
rs2545162	0.82[ASN][1000 genomes]
rs2545164	0.82[ASN][1000 genomes]
rs2545165	0.82[ASN][1000 genomes]
rs2545166	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2545167	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2909786	0.80[ASN][1000 genomes]
rs2909787	0.80[ASN][1000 genomes]
rs2909904	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2909958	0.82[ASN][1000 genomes]
rs2952615	0.82[ASN][1000 genomes]
rs351767	0.97[EUR][1000 genomes]
rs351769	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs351770	0.87[EUR][1000 genomes]
rs351771	0.80[ASN][1000 genomes]
rs35726351	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs372492	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs380144	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs382260	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs386830	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs397768	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs41115	0.80[ASN][1000 genomes]
rs411356	0.83[ASN][1000 genomes]
rs419632	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs42427	0.80[ASN][1000 genomes]
rs429427	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs430665	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs431287	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs433429	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs434090	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs434157	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs438252	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs439456	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs442507	0.82[AMR][1000 genomes]
rs446567	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs454968	0.81[EUR][1000 genomes]
rs455412	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs455469	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs456313	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs458451	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs459102	0.83[EUR][1000 genomes]
rs460301	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs460832	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs461424	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs461866	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs463229	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs464708	0.82[ASN][1000 genomes]
rs465454	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs465899	0.89[ASN][1000 genomes]
rs466443	0.84[ASN][1000 genomes]
rs468101	0.84[AMR][1000 genomes]
rs468783	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs469663	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs469727	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs469760	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs481789	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs495794	0.94[EUR][1000 genomes]
rs497844	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs514763	0.88[EUR][1000 genomes]
rs519397	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs565453	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs565603	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs569940	0.80[ASN][1000 genomes]
rs698405	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs712662	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712663	0.80[EUR][1000 genomes]
rs712664	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712665	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712666	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs712668	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712671	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7213	0.91[EUR][1000 genomes]
rs818423	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs818424	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs818425	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs818426	0.84[ASN][1000 genomes]
rs818427	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs818429	0.83[EUR][1000 genomes]
rs818782	0.80[ASN][1000 genomes]
rs864682	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs866006	0.80[ASN][1000 genomes]
rs9011	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs580237	SRP19	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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