Variant report

Variant	rs12345311
Chromosome Location	chr9:78892863-78892864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10122766	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12335946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17062309	0.91[AFR][1000 genomes]
rs17062312	0.91[AFR][1000 genomes]
rs17062335	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28725352	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57722010	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7037592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7041259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7041527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73652909	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73652910	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73652911	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73652912	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv508552	chr9:78864913-78956326	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv893477	chr9:78892526-78932928	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78883000-78917200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:78889600-78893200	Strong transcription	Fetal Intestine Small	intestine
3	chr9:78889800-78893400	Strong transcription	Fetal Intestine Large	intestine
4	chr9:78891400-78893200	Strong transcription	Duodenum Mucosa	Duodenum

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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