Variant report

Variant	rs3015098
Chromosome Location	chr1:79869873-79869874
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IFI44-2	chr1:79869657-79870246	XLOC_000266
2	lnc-IFI44-2	chr1:79869656-79870246	NONHSAT004088

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10493629	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11162695	0.85[AMR][1000 genomes]
rs11162696	0.85[AMR][1000 genomes]
rs11162697	0.84[AMR][1000 genomes]
rs11578751	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11591000	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12724768	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12726250	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12732505	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12734357	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12745266	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12749113	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12749224	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12760991	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1353290	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1389942	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs1389946	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1389947	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1494852	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1494865	0.83[EUR][1000 genomes]
rs17417360	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17451181	0.88[AMR][1000 genomes]
rs17451905	0.83[EUR][1000 genomes]
rs2029788	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2101800	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2132057	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2860503	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2934873	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2934878	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3000098	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000101	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3000110	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3000133	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3000155	0.85[ASN][1000 genomes]
rs3000174	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3000175	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3000176	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3000177	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3000178	0.90[AMR][1000 genomes]
rs3000179	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015006	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3015008	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3015013	0.82[ASN][1000 genomes]
rs3015025	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3015107	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015108	0.90[AMR][1000 genomes]
rs3015120	0.91[AMR][1000 genomes]
rs33944981	0.85[AMR][1000 genomes]
rs34146004	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34510598	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34554398	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35352017	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35490451	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35676104	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35706038	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35707904	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35733452	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35963120	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36033983	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4414002	0.84[AMR][1000 genomes]
rs4630085	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61767574	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66530141	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6661645	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6692670	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6699018	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7516261	0.82[AMR][1000 genomes]
rs7527570	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7536196	0.86[EUR][1000 genomes]
rs7536365	0.86[EUR][1000 genomes]
rs7555044	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870657	chr1:79701220-79890774	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830337	chr1:79791879-79913241	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv546633	chr1:79794719-79877035	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv871649	chr1:79807447-79924175	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1004014	chr1:79811049-80042309	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv462150	chr1:79835066-79873161	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv546634	chr1:79835066-79873161	Weak transcription Enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv462161	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv462173	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv470721	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv546635	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3015098	USP33	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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