Variant report

Variant	rs73550656
Chromosome Location	chr19:42424510-42424511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr19:42424049-42424641	GM12878	blood:	n/a	n/a
2	POU2F2	chr19:42423934-42424788	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:42423991-42424557	K562	blood:	n/a	n/a
4	NFATC1	chr19:42423924-42424941	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:42423922-42424726	GM12891	blood:	n/a	n/a
6	MYC	chr19:42424275-42424522	MCF-7	breast:	n/a	n/a
7	BCL3	chr19:42423823-42424975	GM12878	blood:	n/a	chr19:42423851-42423864
8	SUZ12	chr19:42423903-42425147	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:42423877-42424905	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:42424004-42424766	GM12878	blood:	n/a	n/a
11	BCL3	chr19:42423878-42424885	GM12878	blood:	n/a	n/a
12	CTCF	chr19:42424489-42424542	GM12891	blood:	n/a	n/a
13	STAT5A	chr19:42423882-42424984	GM12878	blood:	n/a	n/a
14	TCF3	chr19:42423932-42424605	GM12878	blood:	n/a	n/a
15	PBX3	chr19:42424001-42424858	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:42424251-42424687	MCF-7	breast:	n/a	n/a
17	TCF3	chr19:42423896-42424969	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:42424184-42424716	MCF-7	breast:	n/a	n/a
19	POLR2A	chr19:42423890-42424971	GM12891	blood:	n/a	n/a
20	POLR2A	chr19:42423987-42424938	H1-neurons	neurons:	n/a	n/a
21	NR2C2	chr19:42424094-42424920	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:42424113-42424693	H1-neurons	neurons:	n/a	n/a
23	NFATC1	chr19:42423862-42424895	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:42418275..42422419-chr19:42423246..42425922,5	MCF-7	breast:
2	chr19:42416471..42421814-chr19:42422657..42426458,9	K562	blood:
3	chr19:42378499..42381176-chr19:42422747..42425494,2	MCF-7	breast:
4	chr19:42395725..42398076-chr19:42424314..42426348,2	K562	blood:
5	chr19:42401149..42402850-chr19:42422944..42425336,2	K562	blood:
6	chr19:42423745..42425832-chr19:42428186..42430705,2	MCF-7	breast:
7	chr19:42363620..42365789-chr19:42422987..42425618,2	MCF-7	breast:
8	chr19:42385706..42396512-chr19:42423854..42433641,19	K562	blood:
9	chr19:42386835..42388563-chr19:42423995..42426602,2	K562	blood:

No data

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

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11878536	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878555	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881986	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745222	0.85[ASN][1000 genomes]
rs60744864	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60909166	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61422512	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61509766	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550627	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73550630	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73550632	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73550637	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73550639	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550642	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550651	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73550655	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73935809	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[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

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
2	chr19:42421000-42431000	Weak transcription	Dnd41	blood
3	chr19:42421400-42425400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:42422000-42425200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr19:42423200-42424800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:42423400-42425000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr19:42424000-42424800	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:42424200-42425000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:42424400-42425000	ZNF genes & repeats	Spleen	Spleen
10	chr19:42424400-42425600	Enhancers	Gastric	stomach
11	chr19:42424400-42426000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:42424400-42427800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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