Variant report

Variant	rs9848268
Chromosome Location	chr3:48762271-48762272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10865953	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs14018	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4858799	0.95[EUR][1000 genomes]
rs4858800	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4858830	0.95[EUR][1000 genomes]
rs6442129	0.95[EUR][1000 genomes]
rs6442131	0.84[EUR][1000 genomes]
rs6766238	0.84[EUR][1000 genomes]
rs6796790	0.86[EUR][1000 genomes]
rs6801211	0.86[EUR][1000 genomes]
rs6806356	0.96[EUR][1000 genomes]
rs7429596	0.80[EUR][1000 genomes]
rs7610519	0.96[EUR][1000 genomes]
rs7639370	0.81[EUR][1000 genomes]
rs7641050	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9311431	0.81[EUR][1000 genomes]
rs9859473	0.80[EUR][1000 genomes]
rs9873227	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9882443	0.81[AMR][1000 genomes];0.96[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	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9848268	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs9848268	NICN1	cis	Thyroid	GTEx
rs9848268	AMT	cis	Artery Aorta	GTEx
rs9848268	WDR6	cis	Muscle Skeletal	GTEx
rs9848268	AMT	cis	Artery Tibial	GTEx
rs9848268	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs9848268	NICN1-AS1	cis	Thyroid	GTEx
rs9848268	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs9848268	AMT	cis	Adipose Subcutaneous	GTEx
rs9848268	AMT	cis	Thyroid	GTEx
rs9848268	NCKIPSD	cis	Nerve Tibial	GTEx
rs9848268	AMT	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48760600-48765000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:48761600-48764000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:48761600-48764200	Weak transcription	Colonic Mucosa	Colon
4	chr3:48762000-48763800	Weak transcription	Stomach Mucosa	stomach
5	chr3:48762200-48763600	Weak transcription	Rectal Mucosa Donor 31	rectum

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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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