Variant report

Variant	rs3816090
Chromosome Location	chr3:164135957-164135958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 172 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs1073608	0.83[ASN][1000 genomes]
rs1084719	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1084721	0.85[ASN][1000 genomes]
rs11708847	0.87[ASN][1000 genomes]
rs13313898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347398	0.85[ASN][1000 genomes]
rs1435048	0.83[ASN][1000 genomes]
rs1435049	0.83[ASN][1000 genomes]
rs1435050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513445	0.85[ASN][1000 genomes]
rs1513450	0.83[ASN][1000 genomes]
rs1579577	0.83[ASN][1000 genomes]
rs1579578	0.83[ASN][1000 genomes]
rs1579579	0.83[ASN][1000 genomes]
rs1579580	0.83[ASN][1000 genomes]
rs1600082	0.83[ASN][1000 genomes]
rs1606520	0.83[ASN][1000 genomes]
rs1606521	0.83[ASN][1000 genomes]
rs1611924	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1615363	0.83[ASN][1000 genomes]
rs1616240	0.82[ASN][1000 genomes]
rs1623011	0.81[ASN][1000 genomes]
rs1626432	0.83[ASN][1000 genomes]
rs1656094	0.83[ASN][1000 genomes]
rs1656096	0.83[ASN][1000 genomes]
rs1656097	0.83[ASN][1000 genomes]
rs1656098	0.83[ASN][1000 genomes]
rs1656099	0.83[ASN][1000 genomes]
rs1656109	0.83[ASN][1000 genomes]
rs1656110	0.83[ASN][1000 genomes]
rs1656111	0.83[ASN][1000 genomes]
rs1656113	0.83[ASN][1000 genomes]
rs1656114	0.83[ASN][1000 genomes]
rs1656115	0.83[ASN][1000 genomes]
rs1656116	0.83[ASN][1000 genomes]
rs1708469	0.83[ASN][1000 genomes]
rs1708470	0.83[ASN][1000 genomes]
rs1708471	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1708472	0.83[ASN][1000 genomes]
rs1708477	0.85[ASN][1000 genomes]
rs1708482	0.83[ASN][1000 genomes]
rs1708484	0.83[ASN][1000 genomes]
rs1708485	0.83[ASN][1000 genomes]
rs1708486	0.83[ASN][1000 genomes]
rs1708488	0.83[ASN][1000 genomes]
rs1708489	0.83[ASN][1000 genomes]
rs1708490	0.83[ASN][1000 genomes]
rs1708491	0.83[ASN][1000 genomes]
rs1708492	0.83[ASN][1000 genomes]
rs1708493	0.83[ASN][1000 genomes]
rs1708494	0.83[ASN][1000 genomes]
rs1708497	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1708498	0.83[ASN][1000 genomes]
rs1708501	0.82[ASN][1000 genomes]
rs1708502	0.83[ASN][1000 genomes]
rs1708503	0.83[ASN][1000 genomes]
rs1708504	0.82[ASN][1000 genomes]
rs1708505	0.83[ASN][1000 genomes]
rs2117532	0.87[ASN][1000 genomes]
rs2117533	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2117535	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2117536	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141852	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2181	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2182	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28421950	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2886570	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298741	0.83[ASN][1000 genomes]
rs298742	0.83[ASN][1000 genomes]
rs298743	0.83[ASN][1000 genomes]
rs298744	0.83[ASN][1000 genomes]
rs298745	0.83[ASN][1000 genomes]
rs298746	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs298747	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs298755	0.85[ASN][1000 genomes]
rs298756	0.85[ASN][1000 genomes]
rs298757	0.88[ASN][1000 genomes]
rs298758	0.89[ASN][1000 genomes]
rs298759	0.89[ASN][1000 genomes]
rs298760	0.89[ASN][1000 genomes]
rs367230	0.83[ASN][1000 genomes]
rs378206	0.83[ASN][1000 genomes]
rs393334	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs401402	0.83[ASN][1000 genomes]
rs410229	0.82[ASN][1000 genomes]
rs419649	0.82[ASN][1000 genomes]
rs420836	0.83[ASN][1000 genomes]
rs433861	0.83[ASN][1000 genomes]
rs434335	0.83[ASN][1000 genomes]
rs442287	0.83[ASN][1000 genomes]
rs452224	0.83[ASN][1000 genomes]
rs4855177	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4855220	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4855247	0.90[ASN][1000 genomes]
rs66465044	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66685021	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66949604	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67216762	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67336409	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73157132	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7612403	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617240	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618193	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623330	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7623591	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7625665	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626138	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7636354	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7637477	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7638296	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7638502	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7639917	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7639997	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7640767	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7648537	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7650970	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651057	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783583	0.85[ASN][1000 genomes]
rs783584	0.85[ASN][1000 genomes]
rs783585	0.85[ASN][1000 genomes]
rs783586	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs783587	0.85[ASN][1000 genomes]
rs783589	0.85[ASN][1000 genomes]
rs811459	0.85[ASN][1000 genomes]
rs811955	0.85[ASN][1000 genomes]
rs811956	0.85[ASN][1000 genomes]
rs814147	0.85[ASN][1000 genomes]
rs9290232	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs973622	0.81[ASN][1000 genomes]
rs9835203	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835359	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9835558	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9835718	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9839722	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9840047	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9840091	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9844292	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9844690	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9855296	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9864025	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864184	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9865383	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9873142	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876091	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9882072	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs997207	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs999592	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877820	chr3:163557163-164167085	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009069	chr3:163787128-164323219	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv592435	chr3:163832166-164138131	Strong transcription Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877840	chr3:163832988-164200220	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv877887	chr3:163941553-164138131	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1010490	chr3:163961100-164399225	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv497973	chr3:163970658-164370204	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv877892	chr3:163989075-164167085	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1014815	chr3:164007081-164359622	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv877893	chr3:164018044-164202045	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1843213	chr3:164018044-164209573	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1006002	chr3:164021906-164653572	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv877896	chr3:164046501-164138131	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv998340	chr3:164047951-164325380	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv471016	chr3:164088664-164156963	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv1014686	chr3:164123367-164172830	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	nsv1006831	chr3:164123367-164176588	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
18	nsv997482	chr3:164124061-164176588	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	nsv999285	chr3:164133483-164326560	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv536791	chr3:164133483-164326560	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv979794	chr3:164133543-164138805	Enhancers Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3816090	SLITRK3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:164135200-164136400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:164135800-164136400	Enhancers	Rectal Mucosa Donor 31	rectum

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