Variant report

Variant	rs4323773
Chromosome Location	chr1:216598553-216598554
allele	A/G
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	POLR2A	chr1:216598528-216598634	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:216593418..216595910-chr1:216597223..216598829,2	K562	blood:

Variant related genes	Relation type
USH2A	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10779261	0.81[CEU][hapmap]
rs10863240	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10864238	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs10864239	0.87[CHB][hapmap]
rs11117565	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11117568	0.86[CEU][hapmap]
rs11117573	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11117574	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11117575	0.81[CEU][hapmap]
rs11117576	0.81[CEU][hapmap]
rs11120758	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs11120762	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs11590382	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1339962	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs1339963	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs1355630	0.87[CHB][hapmap]
rs1538691	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap]
rs1588657	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs2669053	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs2791292	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2809296	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2809299	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs4078266	0.88[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs4253963	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4396173	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs4488081	0.90[CEU][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs4531347	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4575147	0.88[ASW][hapmap];0.86[CEU][hapmap];0.94[CHB][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap]
rs4846422	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4846428	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6604658	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs6660228	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs6664755	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7518771	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7521264	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7534756	0.91[ASN][1000 genomes]
rs7539376	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7539597	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs7550759	0.82[ASW][hapmap]
rs955942	0.93[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs974601	0.87[CHB][hapmap];0.88[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	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv549199	chr1:216384908-216814702	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1003815	chr1:216504235-216836498	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv535289	chr1:216504235-216836498	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv523863	chr1:216517635-216629416	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216596000-216599000	Weak transcription	Liver	Liver
2	chr1:216597000-216601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:216598400-216598800	Enhancers	Fetal Heart	heart

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