Variant report

Variant	rs11712367
Chromosome Location	chr3:50775446-50775447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 177 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs1013233	0.88[ASN][1000 genomes]
rs10510754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1077215	0.82[CHD][hapmap]
rs11130255	0.94[CEU][hapmap]
rs11130263	0.94[CEU][hapmap]
rs11710858	0.94[CEU][hapmap]
rs11716398	0.89[ASN][1000 genomes]
rs11917538	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]
rs11921011	0.94[CEU][hapmap]
rs11928733	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12487821	0.82[CHD][hapmap]
rs12488948	0.82[CHD][hapmap]
rs12489607	0.82[CHD][hapmap]
rs12495399	0.82[CHD][hapmap]
rs12639126	0.93[CEU][hapmap]
rs12639243	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs129310	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13065995	0.94[CEU][hapmap]
rs13075377	0.94[CEU][hapmap]
rs13088434	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]
rs1379875	0.94[CEU][hapmap]
rs1385025	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs1458385	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[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]
rs1563684	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1598926	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17051043	0.82[CHD][hapmap]
rs17051045	0.82[CHD][hapmap]
rs17051403	0.82[CHD][hapmap]
rs175634	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[YRI][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];0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1947607	0.94[CEU][hapmap]
rs1966920	0.94[CEU][hapmap]
rs1966921	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1971976	0.91[ASN][1000 genomes]
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]
rs2086827	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2125366	0.94[CEU][hapmap]
rs2125369	0.93[CEU][hapmap]
rs2168863	0.94[CEU][hapmap]
rs2168866	0.94[CEU][hapmap]
rs2170840	0.82[LWK][hapmap]
rs2199050	0.94[CEU][hapmap]
rs2219431	0.94[CEU][hapmap]
rs2219432	0.94[CEU][hapmap]
rs2219433	0.94[CEU][hapmap]
rs2232248	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs2262810	0.94[CEU][hapmap]
rs2269505	0.83[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap]
rs2355323	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2355350	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2355697	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2355700	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2355702	0.94[CEU][hapmap]
rs2608988	0.94[CEU][hapmap]
rs2609001	0.94[CEU][hapmap]
rs2609006	0.94[CEU][hapmap]
rs2609020	0.94[CEU][hapmap]
rs2609022	0.94[CEU][hapmap]
rs2609024	0.94[CEU][hapmap]
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]
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]
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]
rs34848480	0.91[ASN][1000 genomes]
rs375544	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];0.81[MKK][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs3792325	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs3792328	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]
rs3804627	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap]
rs3804628	0.94[CEU][hapmap]
rs3804632	0.82[ASN][1000 genomes]
rs3943212	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs396302	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs4078296	0.81[CHD][hapmap]
rs414171	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs417592	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap]
rs4346541	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4346542	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs441516	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4429624	0.94[CEU][hapmap]
rs443436	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs4447760	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs448028	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs4482663	0.93[CEU][hapmap]
rs4485709	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4530518	0.92[CEU][hapmap]
rs453570	0.94[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs4688696	0.81[CHD][hapmap]
rs4688702	0.94[CEU][hapmap]
rs61108141	0.89[EUR][1000 genomes]
rs616589	0.94[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap]
rs616689	0.82[CHD][hapmap];0.82[LWK][hapmap]
rs628081	0.81[JPT][hapmap]
rs6446212	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs6446213	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6446214	0.88[CEU][hapmap]
rs6446220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6446222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6769733	0.87[EUR][1000 genomes]
rs6775012	0.93[CEU][hapmap]
rs6776224	0.93[CEU][hapmap];0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6778680	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6779819	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6791880	0.94[CEU][hapmap]
rs6795573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6796769	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs728901	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs7433217	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs743753	0.82[CHD][hapmap]
rs751851	0.91[ASN][1000 genomes]
rs7611428	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];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7616183	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7621650	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7627266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7629253	0.94[CEU][hapmap]
rs7635666	0.88[ASN][1000 genomes]
rs7638082	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7639301	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7639828	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7642158	0.94[CEU][hapmap]
rs7645212	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7646236	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.80[YRI][hapmap]
rs7650574	0.94[CEU][hapmap]
rs7652715	0.94[CEU][hapmap]
rs808149	0.84[ASN][1000 genomes]
rs809451	0.94[CEU][hapmap]
rs809454	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs813243	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs876104	0.82[CHD][hapmap];0.82[LWK][hapmap]
rs900735	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
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];0.84[ASN][1000 genomes]
rs9820606	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9824444	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9824522	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825535	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9826757	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9831288	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838283	0.94[CEU][hapmap]
rs9839684	0.92[CEU][hapmap]
rs9859692	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9867489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869945	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9875961	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9879397	0.82[CHD][hapmap];0.82[LWK][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11712367	NBEAL2	cis	cerebellum	SCAN
rs11712367	HEMK1	cis	cerebellum	SCAN
rs11712367	TNNC1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50774600-50776000	Enhancers	Brain Substantia Nigra	brain
2	chr3:50774600-50776200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:50774600-50776600	Enhancers	Brain Cingulate Gyrus	brain
4	chr3:50774600-50776800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:50774800-50775600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr3:50774800-50775800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:50774800-50775800	Enhancers	H9 Cell Line	embryonic stem cell
8	chr3:50774800-50775800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:50774800-50776000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr3:50774800-50776000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:50774800-50776000	Enhancers	Brain Hippocampus Middle	brain
12	chr3:50774800-50776600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:50774800-50776800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:50774800-50776800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr3:50774800-50776800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:50774800-50776800	Enhancers	Brain Anterior Caudate	brain
17	chr3:50774800-50777000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:50774800-50777000	Enhancers	Brain Angular Gyrus	brain
19	chr3:50775200-50775600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr3:50775200-50775600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:50775200-50775800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:50775200-50776200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:50775400-50775600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:50775400-50776000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:50775400-50776000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr3:50775400-50777000	Enhancers	Brain Inferior Temporal Lobe	brain

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