Variant report

Variant	rs4485709
Chromosome Location	chr3:50776497-50776498
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 159 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10510754	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs1077215	0.82[CHD][hapmap]
rs11130255	0.94[CEU][hapmap]
rs11130263	0.94[CEU][hapmap]
rs11710858	0.94[CEU][hapmap]
rs11712367	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]
rs11917538	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]
rs11921011	0.94[CEU][hapmap]
rs11928733	0.87[AFR][1000 genomes];0.90[AMR][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	0.81[AMR][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]
rs1458385	0.81[AMR][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]
rs1598926	0.90[AMR][1000 genomes]
rs17051043	0.82[CHD][hapmap]
rs17051045	0.82[CHD][hapmap]
rs17051403	0.82[CHD][hapmap]
rs175634	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[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];0.83[YRI][hapmap]
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]
rs2125366	0.94[CEU][hapmap]
rs2125369	0.93[CEU][hapmap]
rs2168863	0.94[CEU][hapmap]
rs2168866	0.94[CEU][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	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs2355323	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2355350	0.93[AMR][1000 genomes]
rs2355697	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2355700	0.83[AMR][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]
rs375544	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs3792325	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3792328	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs3804627	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs3804628	0.94[CEU][hapmap]
rs3943212	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs396302	0.82[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
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];0.95[MEX][hapmap]
rs4346541	0.81[AMR][1000 genomes]
rs4346542	0.82[AFR][1000 genomes];0.81[AMR][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]
rs448028	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4482663	0.93[CEU][hapmap]
rs4530518	0.92[CEU][hapmap]
rs453570	0.81[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]
rs616589	0.94[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs616689	0.82[CHD][hapmap]
rs628081	0.81[JPT][hapmap]
rs6446212	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap]
rs6446213	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap]
rs6446214	0.88[CEU][hapmap]
rs6446220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs6446222	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];0.93[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes]
rs6775012	0.93[CEU][hapmap]
rs6776224	0.93[CEU][hapmap]
rs6778680	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs6779819	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap]
rs6791880	0.94[CEU][hapmap]
rs6795573	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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]
rs6796769	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap]
rs728901	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs743753	0.82[CHD][hapmap]
rs7611428	0.94[CEU][hapmap]
rs7615703	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap]
rs7621650	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7627266	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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]
rs7629253	0.94[CEU][hapmap]
rs7638082	0.88[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];0.81[AMR][1000 genomes]
rs7639301	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7639828	0.90[AMR][1000 genomes]
rs7642158	0.94[CEU][hapmap]
rs7646236	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs7650574	0.94[CEU][hapmap]
rs7652715	0.94[CEU][hapmap]
rs809451	0.94[CEU][hapmap]
rs809454	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs813243	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs876104	0.82[CHD][hapmap]
rs900735	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs936405	0.94[CEU][hapmap]
rs936406	0.94[CEU][hapmap]
rs9682401	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9820606	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs9824444	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs9824522	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9825535	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[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];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs9826757	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9831288	0.93[AMR][1000 genomes]
rs9838283	0.94[CEU][hapmap]
rs9839684	0.92[CEU][hapmap]
rs9859692	0.81[AMR][1000 genomes]
rs9867489	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9869945	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];0.95[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes]
rs9875961	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs9879397	0.82[CHD][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4485709	NBEAL2	cis	cerebellum	SCAN
rs4485709	TNNC1	cis	cerebellum	SCAN
rs4485709	HEMK1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50774600-50776600	Enhancers	Brain Cingulate Gyrus	brain
2	chr3:50774600-50776800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr3:50774800-50776600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr3:50774800-50776800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:50774800-50776800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:50774800-50776800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:50774800-50776800	Enhancers	Brain Anterior Caudate	brain
8	chr3:50774800-50777000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:50774800-50777000	Enhancers	Brain Angular Gyrus	brain
10	chr3:50775400-50777000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:50775600-50777000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:50775800-50787400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:50776000-50776800	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr3:50776000-50777400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:50776000-50789000	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:50776000-50790000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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