Variant report

Variant	rs4022286
Chromosome Location	chr3:162949279-162949280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTOL1-2	chr3:162948497-162949937	ENSG00000241168.1
2	lnc-OTOL1-2	chr3:162948497-162949934	NONHSAT093026

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10936341	0.87[AFR][1000 genomes]
rs11922496	0.89[AFR][1000 genomes]
rs12330705	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12696185	1.00[ASN][1000 genomes]
rs13079577	0.89[AFR][1000 genomes]
rs1388721	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492171	0.89[AFR][1000 genomes]
rs1813205	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1873644	0.89[AFR][1000 genomes]
rs1994748	0.89[AFR][1000 genomes]
rs1994750	0.89[AFR][1000 genomes]
rs2035871	0.89[AFR][1000 genomes]
rs2172267	0.89[AFR][1000 genomes]
rs2291554	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845224	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853870	0.89[AFR][1000 genomes]
rs3860533	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4323011	0.86[AFR][1000 genomes]
rs4538378	0.87[AFR][1000 genomes]
rs6777137	0.86[AFR][1000 genomes]
rs6780170	0.86[AFR][1000 genomes]
rs6792766	0.89[AFR][1000 genomes]
rs73876636	0.91[EUR][1000 genomes]
rs7427824	0.91[EUR][1000 genomes]
rs7611239	0.89[AFR][1000 genomes]
rs7613401	0.91[EUR][1000 genomes]
rs7624574	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629569	0.89[AFR][1000 genomes]
rs7629602	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641999	0.91[EUR][1000 genomes]
rs7643550	0.86[AFR][1000 genomes]
rs7650512	0.85[EUR][1000 genomes]
rs843056	0.86[AFR][1000 genomes]
rs9809412	0.90[AFR][1000 genomes]
rs9818487	0.86[AFR][1000 genomes]
rs9820908	0.89[AFR][1000 genomes]
rs9833644	0.89[AFR][1000 genomes]
rs9842005	0.87[AFR][1000 genomes]
rs9847195	0.89[AFR][1000 genomes]
rs9852778	0.91[EUR][1000 genomes]
rs9853364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856603	0.89[AFR][1000 genomes]
rs9868682	0.89[AFR][1000 genomes]
rs9869482	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428424	chr3:162145988-163033943	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv592201	chr3:162188625-163142162	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1006015	chr3:162626560-163159978	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877791	chr3:162682825-163267267	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1012835	chr3:162695903-163091909	Enhancers ZNF genes & repeats Active TSS Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv877796	chr3:162839973-162975100	ZNF genes & repeats Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv877797	chr3:162849335-162954568	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv592410	chr3:162857478-162976133	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv2757021	chr3:162861639-162949985	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2759198	chr3:162861639-162949985	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv877799	chr3:162862113-163142162	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv428747	chr3:162883968-163033938	Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv877801	chr3:162887073-162975100	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1006269	chr3:162930989-163324002	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv967190	chr3:162932772-162983278	Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv963286	chr3:162941559-162967897	Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162936400-162950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:162947400-162954200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links