Variant report

Variant	rs12993413
Chromosome Location	chr2:32059410-32059411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:32057686..32060566-chr2:32060880..32062548,2	K562	blood:

Extended variants
information (count: 172 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:169)

rs_ID	r²[population]
rs1005460	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1011309	0.89[ASN][1000 genomes]
rs10153899	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10490357	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490358	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10490359	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11124273	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11681037	0.83[ASN][1000 genomes]
rs11883601	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11884169	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11885062	0.82[EUR][1000 genomes]
rs11887441	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11888094	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11890763	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11893435	0.82[EUR][1000 genomes]
rs11897154	0.83[EUR][1000 genomes]
rs11898765	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11899296	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11901415	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11902241	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11903729	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs12712325	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12988908	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12990358	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12992916	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12993808	0.94[EUR][1000 genomes]
rs12994708	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12994869	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12997171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12997994	0.83[EUR][1000 genomes]
rs13003695	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13005816	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13006751	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13007025	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13013099	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13014501	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13018592	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13021718	0.82[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13022518	0.80[EUR][1000 genomes]
rs13022655	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13022696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13022719	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs13024535	0.85[EUR][1000 genomes]
rs13024644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13028676	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034714	0.84[EUR][1000 genomes]
rs13034933	1.00[CEU][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs13409437	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13414295	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1383023	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs160791	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs160802	0.81[ASW][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs160807	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17011641	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011644	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17011673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17011697	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17011710	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17011711	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17011721	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17011722	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17011740	1.00[CEU][hapmap];0.94[CHD][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs17011742	1.00[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17766509	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17817040	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17817607	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17818002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1808112	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2007608	0.86[ASN][1000 genomes]
rs2064814	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221196	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs221198	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs223620	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs223622	1.00[YRI][hapmap]
rs2366295	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33998544	0.84[EUR][1000 genomes]
rs34056419	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34077616	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34091236	0.80[EUR][1000 genomes]
rs34231321	0.86[EUR][1000 genomes]
rs34316760	0.84[EUR][1000 genomes]
rs34321580	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34369001	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34432107	0.83[EUR][1000 genomes]
rs34437462	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34457675	0.83[EUR][1000 genomes]
rs34460762	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34492168	0.84[EUR][1000 genomes]
rs34497289	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34509832	0.84[EUR][1000 genomes]
rs34540872	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34569213	0.82[EUR][1000 genomes]
rs34617455	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34645083	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34738692	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34776070	0.83[EUR][1000 genomes]
rs34805211	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34893975	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34897620	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34970173	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34973007	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35178826	0.88[ASN][1000 genomes]
rs35179884	0.84[EUR][1000 genomes]
rs35262968	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs35382589	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35397112	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35404750	0.84[EUR][1000 genomes]
rs35439422	0.80[EUR][1000 genomes]
rs35502701	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35514510	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35574090	0.83[EUR][1000 genomes]
rs35631143	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35820518	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36048738	0.93[EUR][1000 genomes]
rs3754837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769607	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs3769614	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3795922	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56821465	0.84[EUR][1000 genomes]
rs62142074	0.87[ASN][1000 genomes]
rs62142076	0.88[ASN][1000 genomes]
rs6543643	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6543644	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66511526	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66522244	0.88[ASN][1000 genomes]
rs66735346	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66863308	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66949767	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67048620	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6718407	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6721692	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6729580	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6733630	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs6736930	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739654	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6746749	0.84[EUR][1000 genomes]
rs67493880	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67517941	0.81[EUR][1000 genomes]
rs67550529	0.85[ASN][1000 genomes]
rs67557317	0.84[EUR][1000 genomes]
rs6755740	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6761760	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761878	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67780569	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67957236	0.85[EUR][1000 genomes]
rs68039196	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68051012	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68076008	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71446027	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71446035	0.84[EUR][1000 genomes]
rs72857279	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72859088	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72860906	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72860941	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72860982	0.88[EUR][1000 genomes]
rs72861000	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7559329	0.86[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs7560472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560714	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562388	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs7574910	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7577579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7587341	0.87[EUR][1000 genomes]
rs7591270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7598154	1.00[CEU][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7601038	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7607030	0.93[EUR][1000 genomes]
rs7607225	0.88[EUR][1000 genomes]
rs875167	1.00[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv873777	chr2:32019747-32197123	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12993413	SLC30A6	cis	parietal	SCAN
rs12993413	CLIP4	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32054400-32080000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:32054600-32067800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:32054600-32090400	Weak transcription	HSMM	muscle
4	chr2:32057200-32117200	Weak transcription	Muscle Satellite Cultured Cells	--

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