Variant report

Variant	rs12084494
Chromosome Location	chr1:216265547-216265548
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	POLR2A	chr1:216265442-216265564	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:216261476..216264118-chr1:216264483..216266208,2	K562	blood:

Variant related genes	Relation type
USH2A	TF binding region
ENSG00000042781	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12083315	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12084498	1.00[MEX][hapmap]
rs12085544	1.00[MEX][hapmap]
rs12090884	0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12093003	0.89[ASW][hapmap];1.00[GIH][hapmap]
rs17026070	0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17026074	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17026077	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17026080	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17026083	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17026096	1.00[GIH][hapmap]
rs17042203	0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55849270	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57958865	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58877005	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60354981	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61445397	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74143941	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74143943	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74143944	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74143945	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74143946	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74143947	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74143955	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv428599	chr1:216086224-216267211	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv873172	chr1:216144827-216281673	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873176	chr1:216249570-216363137	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

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

No data

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