Variant report

Variant	rs2799346
Chromosome Location	chr13:53635280-53635281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2226195	0.90[EUR][1000 genomes]
rs2799347	0.99[EUR][1000 genomes]
rs2799348	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2806967	0.90[EUR][1000 genomes]
rs2806999	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2807004	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886137	0.89[EUR][1000 genomes]
rs9536346	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9568800	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv832613	chr13:53524319-53687188	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53625000-53638800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr13:53632200-53635600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr13:53633200-53636800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:53633200-53642200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:53633600-53636400	Enhancers	Brain Hippocampus Middle	brain
6	chr13:53633600-53636600	Enhancers	Brain Substantia Nigra	brain
7	chr13:53634400-53636200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr13:53634600-53637800	Weak transcription	Pancreas	Pancrea
9	chr13:53634800-53635600	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr13:53634800-53637000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:53635000-53636200	Enhancers	Fetal Brain Male	brain
12	chr13:53635000-53636600	Enhancers	Brain Angular Gyrus	brain
13	chr13:53635000-53637200	Enhancers	Brain Germinal Matrix	brain
14	chr13:53635000-53637600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:53635000-53637800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr13:53635200-53636000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:53635200-53636200	Enhancers	Brain Anterior Caudate	brain
18	chr13:53635200-53636600	Enhancers	Brain Cingulate Gyrus	brain

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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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