Variant report

Variant	rs2041980
Chromosome Location	chr17:66478018-66478019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11868162	0.85[EUR][1000 genomes]
rs11870630	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs16973011	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs55706908	0.84[AMR][1000 genomes]
rs56163561	0.84[AMR][1000 genomes]
rs57006335	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57713835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57970111	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59223374	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62085940	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7207968	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7214330	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72847769	0.84[AMR][1000 genomes]
rs72847771	0.84[AMR][1000 genomes]
rs72847775	0.84[AMR][1000 genomes]
rs72847778	0.84[AMR][1000 genomes]
rs8905	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
2	nsv522271	chr17:66475586-66478018	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2041980	SNORA38B	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66467800-66487000	Weak transcription	Right Atrium	heart
2	chr17:66477000-66480200	Enhancers	HepG2	liver
3	chr17:66477400-66483600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr17:66477600-66479200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:66478000-66478200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:66478000-66478400	Enhancers	Gastric	stomach
7	chr17:66478000-66479600	Enhancers	Ovary	ovary

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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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