Variant report

Variant	rs12029840
Chromosome Location	chr1:114531480-114531481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11102704	0.91[CEU][hapmap]
rs11102712	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1158912	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12029644	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17032048	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2938319	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3006981	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3006996	0.81[AMR][1000 genomes]
rs7520320	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs937672	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12029840	PTPN22	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114523800-114534600	Weak transcription	Primary T cells from cord blood	blood
2	chr1:114527800-114533000	Weak transcription	HSMMtube	muscle
3	chr1:114528000-114533400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:114528000-114536600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:114528200-114535800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:114528200-114540800	Weak transcription	Fetal Lung	lung
7	chr1:114530000-114536200	Weak transcription	Fetal Stomach	stomach
8	chr1:114530200-114533000	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:114531400-114531600	Enhancers	Skeletal Muscle Female	skeletal muscle

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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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