Variant report

Variant	rs11917538
Chromosome Location	chr3:50872976-50872977
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 205 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:204)

rs_ID	r²[population]
rs10510754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1077215	0.82[CHD][hapmap]
rs10865962	0.94[CEU][hapmap]
rs11130255	0.94[CEU][hapmap]
rs11130263	0.94[CEU][hapmap]
rs11130267	0.82[ASW][hapmap];0.94[CEU][hapmap]
rs11710858	0.94[CEU][hapmap]
rs11712367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11715556	0.94[CEU][hapmap]
rs11921011	0.94[CEU][hapmap]
rs11928733	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12487821	0.82[CHD][hapmap]
rs12488948	0.82[CHD][hapmap]
rs12489607	0.82[CHD][hapmap]
rs12491206	0.81[CHD][hapmap]
rs12495399	0.82[CHD][hapmap]
rs12496621	0.82[CHD][hapmap]
rs12639126	0.93[CEU][hapmap]
rs12639243	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062018	0.94[CEU][hapmap]
rs13064199	0.94[CEU][hapmap]
rs13065995	0.94[CEU][hapmap]
rs13069365	0.82[CEU][hapmap]
rs13075377	0.94[CEU][hapmap]
rs13079136	0.94[CEU][hapmap]
rs13079565	0.94[CEU][hapmap]
rs13085827	0.94[CEU][hapmap]
rs13086922	0.94[CEU][hapmap]
rs13088434	0.94[CEU][hapmap]
rs13093289	0.94[CEU][hapmap]
rs13093798	0.94[CEU][hapmap]
rs13094785	0.94[CEU][hapmap]
rs13095920	0.94[CEU][hapmap]
rs13096264	0.94[CEU][hapmap]
rs13096772	0.94[CEU][hapmap]
rs1379873	0.80[EUR][1000 genomes]
rs1379874	0.80[EUR][1000 genomes]
rs1379875	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs1385025	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs1458385	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1458386	0.94[CEU][hapmap]
rs1458387	0.94[CEU][hapmap]
rs1463496	0.94[CEU][hapmap]
rs1463497	0.94[CEU][hapmap]
rs1471177	0.94[CEU][hapmap]
rs1531271	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs1598926	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1598927	0.81[EUR][1000 genomes]
rs1598928	0.80[EUR][1000 genomes]
rs17051043	0.82[CHD][hapmap]
rs17051045	0.82[CHD][hapmap]
rs17051403	0.82[CHD][hapmap]
rs17660513	0.92[CEU][hapmap]
rs1824280	0.94[CEU][hapmap]
rs1824281	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs1841067	0.80[EUR][1000 genomes]
rs1947607	0.94[CEU][hapmap]
rs1966920	0.94[CEU][hapmap]
rs2035484	0.82[CHD][hapmap]
rs2045510	0.93[CEU][hapmap]
rs2045511	0.94[CEU][hapmap]
rs2061388	0.94[CEU][hapmap]
rs2085580	0.94[CEU][hapmap]
rs2085582	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs2085584	0.80[EUR][1000 genomes]
rs2085585	0.80[EUR][1000 genomes]
rs2085586	0.80[EUR][1000 genomes]
rs2125366	0.94[CEU][hapmap]
rs2125369	0.93[CEU][hapmap]
rs2168863	0.94[CEU][hapmap]
rs2168865	0.80[EUR][1000 genomes]
rs2168866	0.94[CEU][hapmap]
rs2199050	0.94[CEU][hapmap]
rs2219431	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs2219432	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs2219433	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2262810	0.94[CEU][hapmap]
rs2355350	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2355697	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2355700	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355702	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2608988	0.94[CEU][hapmap]
rs2608990	0.80[EUR][1000 genomes]
rs2609001	0.94[CEU][hapmap]
rs2609006	0.94[CEU][hapmap]
rs2609016	0.80[EUR][1000 genomes]
rs2609018	0.80[EUR][1000 genomes]
rs2609019	0.80[EUR][1000 genomes]
rs2609020	0.94[CEU][hapmap]
rs2609022	0.94[CEU][hapmap]
rs2609024	0.94[CEU][hapmap]
rs2609028	0.80[EUR][1000 genomes]
rs2609031	0.94[CEU][hapmap]
rs2609036	0.94[CEU][hapmap]
rs2609037	0.94[CEU][hapmap]
rs2675772	0.94[CEU][hapmap]
rs2675773	0.94[CEU][hapmap]
rs2675784	0.80[EUR][1000 genomes]
rs2675792	0.94[CEU][hapmap]
rs2675806	0.94[CEU][hapmap]
rs2675810	0.88[CEU][hapmap]
rs2675812	0.94[CEU][hapmap]
rs2675816	0.90[CEU][hapmap]
rs2675819	0.80[EUR][1000 genomes]
rs2675821	0.80[EUR][1000 genomes]
rs2675822	0.80[EUR][1000 genomes]
rs2675825	0.80[EUR][1000 genomes]
rs2675830	0.94[CEU][hapmap]
rs2675832	0.94[CEU][hapmap]
rs2675834	0.94[CEU][hapmap]
rs2675835	0.94[CEU][hapmap]
rs2675836	0.94[CEU][hapmap]
rs2675837	0.94[CEU][hapmap]
rs2883652	0.94[CEU][hapmap]
rs34628582	0.94[CEU][hapmap]
rs35193996	0.80[EUR][1000 genomes]
rs36057916	0.80[EUR][1000 genomes]
rs3943212	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs396302	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap]
rs4078296	0.81[CHD][hapmap]
rs4132022	0.87[CEU][hapmap]
rs4323036	0.82[CHD][hapmap]
rs4346541	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346542	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429624	0.94[CEU][hapmap]
rs443436	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs4438692	0.94[CEU][hapmap]
rs4443210	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs4447760	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs448028	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs4482663	0.93[CEU][hapmap]
rs4485709	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs4530518	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4688696	0.81[CHD][hapmap]
rs4688702	0.94[CEU][hapmap]
rs61108141	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445717	0.94[CEU][hapmap]
rs6446212	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.80[YRI][hapmap]
rs6446213	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap]
rs6446214	0.88[CEU][hapmap]
rs6446220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6446243	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6446245	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66472954	0.80[EUR][1000 genomes]
rs66684483	0.80[EUR][1000 genomes]
rs67211895	0.80[EUR][1000 genomes]
rs67672341	0.80[EUR][1000 genomes]
rs6769733	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6771085	0.94[CEU][hapmap]
rs6775012	0.93[CEU][hapmap]
rs6776224	0.93[CEU][hapmap];0.81[AFR][1000 genomes]
rs6778680	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6779819	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs6791880	0.94[CEU][hapmap]
rs6795573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6796769	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs6810241	0.94[CEU][hapmap]
rs71329017	0.80[EUR][1000 genomes]
rs728901	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7428086	0.94[CEU][hapmap]
rs7429035	0.94[CEU][hapmap]
rs7433217	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7611428	0.94[CEU][hapmap]
rs7614482	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7614881	0.82[ASW][hapmap];0.94[CEU][hapmap]
rs7615703	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7616183	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621650	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7627266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629253	0.94[CEU][hapmap]
rs7638082	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639301	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7639828	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7642158	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs7650574	0.94[CEU][hapmap]
rs7652715	0.94[CEU][hapmap]
rs876104	0.82[CHD][hapmap]
rs900735	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs936405	0.94[CEU][hapmap]
rs936406	0.94[CEU][hapmap]
rs9682401	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9682672	0.94[CEU][hapmap]
rs9713241	0.93[CEU][hapmap]
rs9758600	0.91[CEU][hapmap]
rs9820606	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9823942	0.94[CEU][hapmap]
rs9824444	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9824522	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9825535	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9826757	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs9831288	0.83[AMR][1000 genomes]
rs9832952	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9837334	1.00[CEU][hapmap]
rs9838283	0.94[CEU][hapmap]
rs9838433	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9839684	0.92[CEU][hapmap]
rs9859692	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9867489	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9868870	0.94[CEU][hapmap]
rs9869945	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875961	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9877272	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9879397	0.82[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11917538	TNNC1	cis	cerebellum	SCAN
rs11917538	HEMK1	cis	cerebellum	SCAN
rs11917538	HEMK1	cis	Lymphoblastoid	GTEx
rs11917538	NBEAL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50868400-50873200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:50869000-50873800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:50869000-50873800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:50871200-50873200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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