Variant report

Variant	rs2081999
Chromosome Location	chr19:42431033-42431034
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:9)
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	RCOR1	chr19:42430992-42431407	K562	blood:	n/a	n/a
2	GATA2	chr19:42430934-42431429	SH-SY5Y	brain:	n/a	n/a
3	CUX1	chr19:42430885-42431140	K562	blood:	n/a	chr19:42430941-42430950
4	ZNF143	chr19:42431000-42431359	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42364213..42366472-chr19:42430072..42433705,3	K562	blood:
2	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
3	chr19:42378071..42380066-chr19:42429626..42432415,2	MCF-7	breast:
4	chr19:42407163..42408726-chr19:42429541..42431369,2	K562	blood:
5	chr19:42430426..42435985-chr19:42461209..42463660,4	K562	blood:
6	chr19:42382327..42390135-chr19:42429723..42437438,12	MCF-7	breast:
7	chr19:42365213..42368096-chr19:42429393..42431288,2	K562	blood:
8	chr19:42429855..42432360-chr19:42434801..42438430,3	MCF-7	breast:
9	chr19:42385706..42396512-chr19:42423854..42433641,19	K562	blood:

No data

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000105404	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10409822	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10411814	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414709	0.84[ASN][1000 genomes]
rs10416501	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10419731	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420264	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10424013	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11083642	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11665965	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11667048	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668332	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669448	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11878287	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12971376	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975677	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1864207	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1965727	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745223	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826707	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61007366	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246830	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247727	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7253563	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs735571	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109192	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919390	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9304600	0.85[EUR][1000 genomes]
rs9676662	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9749440	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2081999	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs2081999	RABAC1	cis	multi-tissue	Pritchard

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42425600-42432400	Weak transcription	Gastric	stomach
2	chr19:42426600-42431600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr19:42426800-42431600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:42427800-42431200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr19:42427800-42431600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr19:42427800-42431600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr19:42429000-42432400	Weak transcription	Pancreas	Pancrea
8	chr19:42430600-42433000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:42431000-42431200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr19:42431000-42431200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:42431000-42431400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:42431000-42431600	Bivalent Enhancer	Primary B cells from cord blood	blood
13	chr19:42431000-42431800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr19:42431000-42431800	Enhancers	Dnd41	blood
15	chr19:42431000-42431800	Enhancers	K562	blood

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