Variant report

Variant	rs58880408
Chromosome Location	chr2:128204215-128204216
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10201047	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10496663	0.86[EUR][1000 genomes]
rs10928765	0.88[EUR][1000 genomes]
rs10928766	0.89[EUR][1000 genomes]
rs10928769	0.86[EUR][1000 genomes]
rs11679431	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680815	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11682864	0.86[EUR][1000 genomes]
rs11690086	0.86[EUR][1000 genomes]
rs11892245	0.81[ASN][1000 genomes]
rs11900469	0.89[EUR][1000 genomes]
rs12053309	0.86[EUR][1000 genomes]
rs12618494	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12619972	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12623334	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13011041	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13389029	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1568277	0.87[EUR][1000 genomes]
rs1568279	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17015274	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732205	0.86[EUR][1000 genomes]
rs3889307	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56106399	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62160265	0.88[EUR][1000 genomes]
rs62160266	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62160287	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62160288	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62160289	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62160291	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66609069	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6716489	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67495946	0.87[EUR][1000 genomes]
rs7586672	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs880933	0.84[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	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv519035	chr2:128195244-128210400	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv524607	chr2:128196424-128218364	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs58880408	AC068282.3	cis	Nerve Tibial	GTEx
rs58880408	AC068282.3	cis	Whole Blood	GTEx
rs58880408	AC068282.3	cis	Esophagus Muscularis	GTEx
rs58880408	AC068282.3	cis	Stomach	GTEx
rs58880408	AC068282.3	cis	lung	GTEx
rs58880408	MAP3K2	cis	multi-tissue	Pritchard
rs58880408	AC068282.3	cis	Thyroid	GTEx
rs58880408	AC068282.3	cis	Esophagus Mucosa	GTEx
rs58880408	AC068282.3	cis	Muscle Skeletal	GTEx
rs58880408	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs58880408	AC068282.3	cis	Artery Tibial	GTEx
rs58880408	AC068282.3	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128181400-128209800	Weak transcription	Right Atrium	heart
2	chr2:128196200-128211600	Weak transcription	Colonic Mucosa	Colon
3	chr2:128203200-128206800	Weak transcription	Primary T cells from cord blood	blood
4	chr2:128203800-128206000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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