Variant report

Variant	rs10402825
Chromosome Location	chr19:42213744-42213745
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10415940	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12971352	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28683503	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34155934	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35091611	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3928915	0.89[AMR][1000 genomes]
rs3928918	0.83[AMR][1000 genomes]
rs3928919	0.83[AMR][1000 genomes]
rs7250222	0.83[AMR][1000 genomes]
rs7256221	0.85[EUR][1000 genomes]
rs7257798	0.86[EUR][1000 genomes]
rs7258524	0.82[EUR][1000 genomes]
rs7259215	0.86[EUR][1000 genomes]
rs889365	0.86[EUR][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	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	nsv1061309	chr19:42187716-42228445	Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv978820	chr19:42212524-42214379	Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv482220	chr19:42212530-42234436	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3425986	chr19:42212540-42259719	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42211000-42214200	Active TSS	Rectal Smooth Muscle	rectum
2	chr19:42212000-42216200	Active TSS	Esophagus	oesophagus
3	chr19:42212000-42222800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:42212400-42213800	Active TSS	Colonic Mucosa	Colon
5	chr19:42212400-42214400	Active TSS	Stomach Mucosa	stomach
6	chr19:42212600-42214000	Active TSS	Small Intestine	intestine
7	chr19:42212600-42215200	Active TSS	Fetal Intestine Small	intestine
8	chr19:42212800-42213800	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr19:42213000-42215000	Active TSS	Fetal Stomach	stomach
10	chr19:42213600-42214000	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr19:42213600-42217200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum

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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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