Variant report

Variant	rs2286476
Chromosome Location	chr19:38850759-38850760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38843850..38848913-chr19:38849820..38852865,6	K562	blood:
2	chr19:38850348..38855103-chr19:38862504..38867180,11	K562	blood:
3	chr19:38826255..38829380-chr19:38850634..38854376,3	MCF-7	breast:
4	chr19:38849999..38854779-chr19:38863669..38868606,10	K562	blood:
5	chr19:38849976..38851523-chr19:38865521..38867449,2	MCF-7	breast:
6	chr19:38846299..38848988-chr19:38850348..38854198,4	MCF-7	breast:
7	chr19:38845897..38848818-chr19:38850039..38852720,3	K562	blood:
8	chr19:38718872..38720876-chr19:38850703..38853087,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000011332	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000099338	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11671779	0.84[CEU][hapmap]
rs11673012	0.84[CEU][hapmap]
rs11673222	0.84[CEU][hapmap]
rs11880532	0.84[CHD][hapmap]
rs11881305	0.81[CEU][hapmap];0.95[GIH][hapmap];0.82[LWK][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap]
rs12609247	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.83[LWK][hapmap];0.91[EUR][1000 genomes]
rs12609878	0.82[CHD][hapmap]
rs12611255	0.86[EUR][1000 genomes]
rs2270094	0.84[CEU][hapmap]
rs2270095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286475	1.00[CEU][hapmap];0.93[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2304176	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs3178327	0.81[CEU][hapmap];0.93[GIH][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap]
rs3745951	0.84[CEU][hapmap]
rs3815345	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3843754	0.81[CEU][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap]
rs4312417	0.81[CEU][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap]
rs4386247	0.84[CEU][hapmap]
rs4802324	0.87[TSI][hapmap]
rs4804046	0.84[CEU][hapmap]
rs56849284	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57618695	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58728151	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59898212	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60071299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61160177	0.89[EUR][1000 genomes]
rs7252835	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253960	0.89[EUR][1000 genomes]
rs73043010	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73043037	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106900	0.88[CEU][hapmap]
rs8112211	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes]
rs931749	0.84[CEU][hapmap]
rs931750	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2286476	PSG4	cis	cerebellum	SCAN
rs2286476	LOC390940	cis	parietal	SCAN
rs2286476	APOC4	cis	cerebellum	SCAN
rs2286476	C19orf33	cis	normal skin	skin_eQTL
rs2286476	SELV	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38828200-38852000	Weak transcription	Right Atrium	heart
2	chr19:38835200-38852000	Weak transcription	Pancreas	Pancrea
3	chr19:38849400-38851800	Weak transcription	Lung	lung
4	chr19:38850400-38851800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:38850600-38851800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast

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