Variant report

Variant	rs56049603
Chromosome Location	chr3:49585243-49585244
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10865956	0.84[EUR][1000 genomes]
rs11928090	0.83[EUR][1000 genomes]
rs12583	0.84[EUR][1000 genomes]
rs13322887	0.83[EUR][1000 genomes]
rs1982861	0.86[EUR][1000 genomes]
rs2312462	0.83[EUR][1000 genomes]
rs3866330	0.83[EUR][1000 genomes]
rs3870341	0.84[EUR][1000 genomes]
rs3905330	0.82[EUR][1000 genomes]
rs4052546	0.84[EUR][1000 genomes]
rs4241407	0.83[EUR][1000 genomes]
rs4855837	0.81[EUR][1000 genomes]
rs4855853	0.82[EUR][1000 genomes]
rs56324858	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62261183	0.80[EUR][1000 genomes]
rs62261249	0.83[EUR][1000 genomes]
rs6783003	0.80[EUR][1000 genomes]
rs72934271	0.80[EUR][1000 genomes]
rs73073004	0.87[EUR][1000 genomes]
rs7355800	0.80[EUR][1000 genomes]
rs7613491	0.80[EUR][1000 genomes]
rs7625857	0.81[EUR][1000 genomes]
rs7644148	0.81[EUR][1000 genomes]
rs7647973	0.80[EUR][1000 genomes]
rs9860055	0.80[EUR][1000 genomes]
rs9862534	0.83[EUR][1000 genomes]
rs9871024	0.83[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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs56049603	AMT	cis	lung	GTEx
rs56049603	NICN1-AS1	cis	Thyroid	GTEx
rs56049603	WDR6	cis	Nerve Tibial	GTEx
rs56049603	AMT	cis	Esophagus Mucosa	GTEx
rs56049603	AMT	cis	Whole Blood	GTEx
rs56049603	AMT	cis	Adipose Subcutaneous	GTEx
rs56049603	AMT	cis	Thyroid	GTEx
rs56049603	WDR6	cis	Muscle Skeletal	GTEx
rs56049603	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs56049603	AMT	cis	Nerve Tibial	GTEx
rs56049603	AMT	cis	Muscle Skeletal	GTEx
rs56049603	AMT	cis	Artery Tibial	GTEx
rs56049603	NICN1	cis	Thyroid	GTEx
rs56049603	AMT	cis	Artery Aorta	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49584800-49585400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49585000-49585400	Enhancers	H1 Cell Line	embryonic stem cell
3	chr3:49585000-49585800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:49585200-49585400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:49585200-49590600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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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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