Variant report

Variant	rs11878555
Chromosome Location	chr19:42423751-42423752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr19:42422230-42423775	A549	lung:	n/a	n/a

No data

(count:7 , 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	chr19:42401149..42402850-chr19:42422944..42425336,2	K562	blood:
5	chr19:42423745..42425832-chr19:42428186..42430705,2	MCF-7	breast:
6	chr19:42363620..42365789-chr19:42422987..42425618,2	MCF-7	breast:
7	chr19:42412650..42414270-chr19:42421540..42424383,2	MCF-7	breast:

No data

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000076928	Chromatin interaction
ENSG00000268041	Chromatin interaction
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10403081	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10417495	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs10419314	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11878536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881986	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12104228	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs16975619	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2288509	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2288512	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2303798	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs28521795	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs3745222	0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs60744864	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60909166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61422512	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61509766	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs717225	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7253691	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap]
rs7260129	1.00[YRI][hapmap]
rs73550627	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73550630	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73550632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73550637	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73550639	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550651	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73550655	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73550656	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935809	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110305	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8113339	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs8113686	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs891172	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]

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:9 , 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	chr19:42423400-42424400	Weak transcription	Gastric	stomach
7	chr19:42423400-42425000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr19:42423600-42423800	ZNF genes & repeats	Spleen	Spleen
9	chr19:42423600-42424200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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