Variant report

Variant	rs2286550
Chromosome Location	chr19:38861362-38861363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr19:38860838-38861460	K562	blood:	n/a	n/a
2	MYC	chr19:38860961-38861376	K562	blood:	n/a	n/a
3	GATA2	chr19:38860862-38861484	K562	blood:	n/a	chr19:38861049-38861059
4	TAL1	chr19:38860914-38861368	K562	blood:	n/a	n/a
5	ELF1	chr19:38861143-38861495	K562	blood:	n/a	chr19:38861308-38861321
6	GATA2	chr19:38860989-38861443	K562	blood:	n/a	chr19:38861049-38861059
7	PML	chr19:38860836-38861401	K562	blood:	n/a	n/a
8	CEBPB	chr19:38861113-38861386	K562	blood:	n/a	n/a
9	YY1	chr19:38861112-38861436	K562	blood:	n/a	n/a
10	GABPA	chr19:38860926-38861438	K562	blood:	n/a	n/a
11	CEBPD	chr19:38860977-38861369	K562	blood:	n/a	n/a
12	TRIM28	chr19:38860915-38861431	K562	blood:	n/a	n/a
13	TEAD4	chr19:38860900-38861395	K562	blood:	n/a	n/a
14	CEBPD	chr19:38860899-38861440	K562	blood:	n/a	n/a
15	MAX	chr19:38860817-38861461	K562	blood:	n/a	chr19:38860939-38860948
16	POLR2A	chr19:38860918-38861377	K562	blood:	n/a	n/a
17	CBX3	chr19:38860889-38861399	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:38728291..38731006-chr19:38860987..38862689,2	K562	blood:
2	chr19:38745762..38747898-chr19:38860453..38862008,2	K562	blood:
3	chr19:38824978..38827447-chr19:38860832..38862469,2	MCF-7	breast:
4	chr19:38860843..38863551-chr19:38863957..38866208,2	MCF-7	breast:
5	chr19:38861029..38862788-chr19:38863636..38866325,2	K562	blood:

No data

Variant related genes	Relation type
PSMD8	TF binding region
ENSG00000099341	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000167641	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1060455	1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11083453	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11878707	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs12460181	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12460264	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12460599	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12461248	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12461700	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12462230	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12463175	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072350	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2074979	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2074980	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286547	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286551	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2302226	0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35848839	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745955	0.99[ASN][1000 genomes]
rs3745956	1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3745960	0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3745961	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3745962	0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3745964	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3859550	0.82[CHB][hapmap]
rs4802399	1.00[JPT][hapmap]
rs4802400	0.80[MEX][hapmap]
rs60577771	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60759642	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60915799	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61379500	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2286550	SPINT2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38853800-38864400	Weak transcription	A549	lung
2	chr19:38860400-38861600	Enhancers	K562	blood
3	chr19:38860600-38861400	Enhancers	Duodenum Mucosa	Duodenum
4	chr19:38861200-38865000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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