Variant report

Variant	rs380144
Chromosome Location	chr5:112195992-112195993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:112195942-112197882	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:112195946-112198491	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:112195601-112197435	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:112195959-112198286	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112195906..112198557-chr5:112198644..112200582,4	MCF-7	breast:
2	chr5:112195408..112199487-chr5:112199566..112202603,4	K562	blood:
3	chr5:112195538..112198310-chr5:112312375..112313895,2	K562	blood:
4	chr5:112195332..112197808-chr5:112240725..112243513,2	K562	blood:
5	chr5:112172653..112174509-chr5:112195056..112196675,2	MCF-7	breast:
6	chr5:112041706..112044186-chr5:112195413..112197519,3	MCF-7	breast:
7	chr5:112194408..112196977-chr5:112198175..112200544,3	MCF-7	breast:
8	chr5:112152202..112156283-chr5:112195630..112198484,4	MCF-7	breast:
9	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:
10	chr5:112188139..112189765-chr5:112194415..112196734,2	K562	blood:

No data

Variant related genes	Relation type
SRP19	TF binding region
ENSG00000272869	TF binding region
ENSG00000153037	Chromatin interaction
ENSG00000134982	Chromatin interaction
ENSG00000129625	Chromatin interaction
ENSG00000172795	Chromatin interaction
ENSG00000266499	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1069061	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1093611	0.82[EUR][1000 genomes]
rs1093677	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs151976	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs151977	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs151978	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs153545	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs153546	0.82[EUR][1000 genomes]
rs153562	0.81[AMR][1000 genomes]
rs193527	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2545163	0.83[ASN][1000 genomes]
rs2545166	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2545167	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2545169	0.86[ASN][1000 genomes]
rs2545751	0.94[ASN][1000 genomes]
rs2546111	0.81[ASN][1000 genomes]
rs2909904	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs351767	0.97[EUR][1000 genomes]
rs351769	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs351770	0.87[EUR][1000 genomes]
rs35726351	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs372492	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs382260	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs392907	0.81[ASN][1000 genomes]
rs395266	0.81[ASN][1000 genomes]
rs419632	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs429427	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs430665	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs431287	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs434090	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs434157	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs438252	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439456	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs442507	0.84[AMR][1000 genomes]
rs446567	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs454968	0.80[EUR][1000 genomes]
rs455412	0.83[EUR][1000 genomes]
rs455469	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs456313	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs458451	0.83[EUR][1000 genomes]
rs459102	0.83[EUR][1000 genomes]
rs459552	0.85[ASN][1000 genomes]
rs460301	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs460832	0.83[EUR][1000 genomes]
rs461424	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs461866	0.84[AMR][1000 genomes]
rs463229	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs465454	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs468101	0.86[AMR][1000 genomes]
rs468783	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs469663	0.84[AMR][1000 genomes]
rs469727	0.86[AMR][1000 genomes]
rs469760	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs481789	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs495794	0.94[EUR][1000 genomes]
rs497844	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs501250	0.81[ASN][1000 genomes]
rs514763	0.88[EUR][1000 genomes]
rs519397	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs529076	0.81[ASN][1000 genomes]
rs544243	0.85[ASN][1000 genomes]
rs563556	0.81[ASN][1000 genomes]
rs565453	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs565603	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs580237	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs698405	0.86[AMR][1000 genomes]
rs712662	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs712663	0.80[EUR][1000 genomes]
rs712664	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs712665	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs712666	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs712668	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712671	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7213	0.91[EUR][1000 genomes]
rs818423	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs818424	0.81[EUR][1000 genomes]
rs818425	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs818427	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs818429	0.83[EUR][1000 genomes]
rs864682	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9011	0.86[AMR][1000 genomes];0.92[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	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	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
4	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
5	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
rs380144	SRP19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 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
5	chr5:112195800-112196200	Enhancers	Dnd41	blood

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