Variant report

Variant	rs11883601
Chromosome Location	chr2:31989586-31989587
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 147 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs1005460	0.85[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1011309	0.80[ASN][1000 genomes]
rs10153899	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10204002	0.80[EUR][1000 genomes]
rs10490357	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10490358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10490359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11124267	0.91[EUR][1000 genomes]
rs11124273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11884169	0.91[EUR][1000 genomes]
rs11885062	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11888094	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11890763	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11898765	0.81[EUR][1000 genomes]
rs11901415	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11902241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs12712325	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12988908	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12993413	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12993808	0.80[EUR][1000 genomes]
rs12994708	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12997171	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12997994	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13001512	0.95[EUR][1000 genomes]
rs13003695	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13005816	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs13006356	0.92[EUR][1000 genomes]
rs13006358	0.93[EUR][1000 genomes]
rs13006751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13007025	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13013099	0.92[EUR][1000 genomes]
rs13014501	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13018592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13021718	0.82[CHD][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap]
rs13022655	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13022696	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13022719	0.82[EUR][1000 genomes]
rs13024535	0.88[EUR][1000 genomes]
rs13024644	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap]
rs13027103	0.85[EUR][1000 genomes]
rs13028676	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13034714	0.87[EUR][1000 genomes]
rs13395648	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs13414295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1383023	0.89[ASW][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs160791	0.86[ASN][1000 genomes]
rs160807	0.87[ASN][1000 genomes]
rs17011641	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17011644	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17011673	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17011697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17011710	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17011711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17011721	0.83[EUR][1000 genomes]
rs17011722	0.91[EUR][1000 genomes]
rs17766509	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17817040	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17817607	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17818002	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2064814	0.92[EUR][1000 genomes]
rs221196	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs221198	0.83[ASN][1000 genomes]
rs223620	0.86[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs2366295	0.83[ASN][1000 genomes]
rs33998544	0.87[EUR][1000 genomes]
rs34056419	0.92[EUR][1000 genomes]
rs34077616	0.91[EUR][1000 genomes]
rs34091236	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34124115	0.84[EUR][1000 genomes]
rs34231321	0.89[EUR][1000 genomes]
rs34316760	0.87[EUR][1000 genomes]
rs34369001	0.92[EUR][1000 genomes]
rs34492168	0.87[EUR][1000 genomes]
rs34509832	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34540872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34617455	0.92[EUR][1000 genomes]
rs34645083	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34687527	0.90[EUR][1000 genomes]
rs34738692	0.91[EUR][1000 genomes]
rs34776070	0.85[EUR][1000 genomes]
rs34805211	0.95[EUR][1000 genomes]
rs34893975	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34970173	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34973007	0.92[EUR][1000 genomes]
rs35118236	0.83[EUR][1000 genomes]
rs35179884	0.87[EUR][1000 genomes]
rs35262968	0.87[EUR][1000 genomes]
rs35382589	0.91[EUR][1000 genomes]
rs35397112	0.89[EUR][1000 genomes]
rs35404750	0.87[EUR][1000 genomes]
rs35439422	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35502701	0.92[EUR][1000 genomes]
rs35514510	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35574090	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35631143	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35820518	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754837	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3754838	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap]
rs3769614	0.84[EUR][1000 genomes]
rs3795922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3819844	0.82[EUR][1000 genomes]
rs479847	0.82[EUR][1000 genomes]
rs56821465	0.87[EUR][1000 genomes]
rs57754448	0.90[EUR][1000 genomes]
rs6543643	0.82[ASN][1000 genomes]
rs6543644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs66511526	0.92[EUR][1000 genomes]
rs66735346	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66949767	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67048620	0.92[EUR][1000 genomes]
rs6721692	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6729580	0.81[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67335141	0.82[EUR][1000 genomes]
rs6733630	0.87[EUR][1000 genomes]
rs6736930	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6739654	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6746749	0.87[EUR][1000 genomes]
rs67493880	0.83[EUR][1000 genomes]
rs67557317	0.87[EUR][1000 genomes]
rs6761760	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6761878	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67780569	0.92[EUR][1000 genomes]
rs67957236	0.88[EUR][1000 genomes]
rs68039196	0.91[EUR][1000 genomes]
rs68051012	0.95[EUR][1000 genomes]
rs71446026	0.82[EUR][1000 genomes]
rs71446027	0.92[EUR][1000 genomes]
rs71446035	0.87[EUR][1000 genomes]
rs72857279	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72859088	0.92[EUR][1000 genomes]
rs72860906	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72860941	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72861000	0.87[EUR][1000 genomes]
rs7559329	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs7560472	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7560714	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7562326	0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap]
rs7577579	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs7589579	0.85[EUR][1000 genomes]
rs7591270	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7594951	0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs7607225	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1002988	chr2:31767131-31996924	Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3376782	chr2:31861607-32046180	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1003376	chr2:31889934-32022595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1015021	chr2:31972738-32030696	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11883601	SLC30A6	cis	parietal	SCAN
rs11883601	CLIP4	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31988800-31990400	Enhancers	Fetal Brain Male	brain
2	chr2:31989000-31990000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:31989000-31990400	Enhancers	NHEK	skin
4	chr2:31989000-31990600	Enhancers	Fetal Intestine Large	intestine
5	chr2:31989200-31989600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:31989200-31990000	Enhancers	Fetal Muscle Leg	muscle
7	chr2:31989400-31990200	Weak transcription	Fetal Intestine Small	intestine
8	chr2:31989400-31990600	Weak transcription	Fetal Kidney	kidney

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