Variant report

Variant	rs12620828
Chromosome Location	chr2:67806472-67806473
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10184721	0.87[ASN][1000 genomes]
rs2861699	0.89[LWK][hapmap];1.00[YRI][hapmap]
rs2902024	0.87[ASN][1000 genomes]
rs6546318	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6546323	0.89[LWK][hapmap];1.00[YRI][hapmap]
rs7579880	0.83[AFR][1000 genomes]
rs7582772	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12620828	NAGK	cis	cerebellum	SCAN
rs12620828	VAX2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67805400-67807800	Enhancers	Fetal Lung	lung
2	chr2:67806000-67806800	Enhancers	Fetal Stomach	stomach
3	chr2:67806000-67807000	Enhancers	NHLF	lung
4	chr2:67806200-67807200	Enhancers	Dnd41	blood
5	chr2:67806200-67807400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:67806200-67807600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:67806400-67807000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:67806400-67807000	Enhancers	Small Intestine	intestine

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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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