Variant report

Variant	rs11209853
Chromosome Location	chr1:72305762-72305763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr1:72305516-72305936	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr1:72305367-72306002	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr1:72305436-72306027	SH-SY5Y	brain:	n/a	n/a
4	EP300	chr1:72305240-72306317	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr1:72305464-72306002	SK-N-SH	brain:	n/a	n/a
6	EP300	chr1:72305569-72305989	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
NEGR1-IT1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11209851	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11209852	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11209862	0.81[CHB][hapmap]
rs11209863	0.81[CHB][hapmap]
rs11209864	0.80[CHB][hapmap]
rs11209865	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs11209867	0.81[CHB][hapmap]
rs11579239	0.81[CHB][hapmap]
rs12025922	1.00[ASW][hapmap];0.81[CHB][hapmap]
rs12037610	0.88[EUR][1000 genomes]
rs12039773	0.81[CHB][hapmap]
rs12045130	0.81[CHB][hapmap]
rs12562379	0.81[CHB][hapmap]
rs12749167	0.81[CHB][hapmap]
rs1350648	0.82[CEU][hapmap]
rs1426178	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1426179	0.81[CHB][hapmap]
rs17091876	0.85[CHB][hapmap]
rs1814054	0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs1814055	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851882	0.80[CHB][hapmap];0.81[YRI][hapmap]
rs3909664	0.81[CHB][hapmap]
rs495411	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs508954	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs510012	0.81[EUR][1000 genomes]
rs517762	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs517901	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs545538	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs546741	0.91[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs626185	0.81[CHB][hapmap]
rs6659202	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6660086	0.81[CHB][hapmap]
rs6683448	0.82[CEU][hapmap]
rs7526542	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7529181	0.90[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949599	chr1:71655652-72327802	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1007250	chr1:71998391-72350683	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv534992	chr1:71998391-72350683	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv948821	chr1:72049987-72477221	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1003446	chr1:72060680-72419918	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1008210	chr1:72099161-72374197	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv2762150	chr1:72271227-72395953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv870762	chr1:72300968-72376262	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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