Variant report

Variant	rs6446245
Chromosome Location	chr3:51037258-51037259
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 161 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs10510754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10865962	0.94[CEU][hapmap]
rs11130263	0.94[CEU][hapmap]
rs11130267	0.82[ASW][hapmap];0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs11130280	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap]
rs11715556	0.94[CEU][hapmap]
rs11917538	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]
rs11919932	0.94[CEU][hapmap]
rs11921011	0.94[CEU][hapmap]
rs11928733	0.83[EUR][1000 genomes]
rs12494165	0.88[ASW][hapmap];0.94[CEU][hapmap]
rs12639243	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13061003	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs13062018	0.94[CEU][hapmap]
rs13064199	0.94[CEU][hapmap]
rs13065995	0.94[CEU][hapmap]
rs13069365	0.82[CEU][hapmap]
rs13079136	0.94[CEU][hapmap]
rs13079565	0.94[CEU][hapmap]
rs13080170	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][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]
rs13324500	0.94[CEU][hapmap]
rs1379875	0.94[CEU][hapmap]
rs1458385	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1471177	0.94[CEU][hapmap]
rs1531271	0.94[CEU][hapmap]
rs1598926	0.83[EUR][1000 genomes]
rs17660513	0.92[CEU][hapmap]
rs1947607	0.94[CEU][hapmap]
rs1966920	0.94[CEU][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]
rs2168863	0.94[CEU][hapmap]
rs2219431	0.94[CEU][hapmap]
rs2219432	0.94[CEU][hapmap]
rs2219433	0.94[CEU][hapmap]
rs2355350	0.82[EUR][1000 genomes]
rs2355697	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2355700	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2355702	0.94[CEU][hapmap]
rs2609020	0.94[CEU][hapmap]
rs2609022	0.94[CEU][hapmap]
rs2609031	0.94[CEU][hapmap]
rs2609037	0.94[CEU][hapmap]
rs2675792	0.94[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]
rs34628582	0.94[CEU][hapmap]
rs4132022	0.87[CEU][hapmap]
rs4244696	0.94[CEU][hapmap]
rs4244704	0.94[CEU][hapmap]
rs4263323	0.94[CEU][hapmap]
rs4267675	0.94[CEU][hapmap]
rs4286453	0.94[CEU][hapmap]
rs4309763	0.94[CEU][hapmap]
rs4346541	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4346542	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4356848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4373098	0.94[CEU][hapmap]
rs4377512	0.94[CEU][hapmap]
rs4438692	0.94[CEU][hapmap]
rs4443210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4446244	0.94[CEU][hapmap]
rs4447760	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4475072	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs4478114	0.94[CEU][hapmap]
rs4488874	0.94[CEU][hapmap]
rs4505743	0.94[CEU][hapmap]
rs4511931	0.94[CEU][hapmap]
rs4511933	0.94[CEU][hapmap]
rs4530518	0.92[CEU][hapmap]
rs4530566	0.94[CEU][hapmap]
rs4555554	0.93[CEU][hapmap]
rs4560329	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs4566574	0.94[CEU][hapmap]
rs4572801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs4582086	0.94[CEU][hapmap]
rs4586853	0.94[CEU][hapmap]
rs4589968	0.94[CEU][hapmap]
rs4615113	0.94[CEU][hapmap]
rs4927960	0.94[CEU][hapmap]
rs4927970	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4927978	0.94[CEU][hapmap]
rs4927983	0.94[CEU][hapmap]
rs61108141	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6445600	0.94[CEU][hapmap]
rs6445717	0.94[CEU][hapmap]
rs6445750	0.94[CEU][hapmap]
rs6445779	0.94[CEU][hapmap]
rs6445802	0.91[CEU][hapmap]
rs6446011	0.94[CEU][hapmap]
rs6446118	0.94[CEU][hapmap]
rs6446167	0.94[CEU][hapmap]
rs6446168	0.94[CEU][hapmap]
rs6446220	0.82[EUR][1000 genomes]
rs6446222	0.83[EUR][1000 genomes]
rs6446243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6768601	0.94[CEU][hapmap]
rs6769733	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6771085	0.94[CEU][hapmap]
rs6772197	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6784455	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs6787773	0.94[CEU][hapmap]
rs6787805	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap]
rs6793613	0.94[CEU][hapmap]
rs6793648	0.94[CEU][hapmap]
rs6795272	0.88[ASW][hapmap];0.94[CEU][hapmap]
rs6795573	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6810241	0.94[CEU][hapmap]
rs7428086	0.94[CEU][hapmap]
rs7429035	0.94[CEU][hapmap]
rs7433217	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[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];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611873	0.94[CEU][hapmap]
rs7614171	0.94[CEU][hapmap]
rs7614482	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7614881	0.82[ASW][hapmap];0.94[CEU][hapmap]
rs7615291	0.94[CEU][hapmap]
rs7616183	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621650	0.82[EUR][1000 genomes]
rs7627266	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7629420	0.94[CEU][hapmap]
rs7629433	0.94[CEU][hapmap]
rs7638082	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7638732	0.88[ASW][hapmap];0.94[CEU][hapmap]
rs7639301	0.83[EUR][1000 genomes]
rs7639828	0.82[EUR][1000 genomes]
rs7640263	0.93[CEU][hapmap]
rs7642158	0.94[CEU][hapmap]
rs7652655	0.94[CEU][hapmap]
rs7652818	0.94[CEU][hapmap]
rs7653451	0.94[CEU][hapmap]
rs9681865	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9682672	0.94[CEU][hapmap]
rs9713241	0.93[CEU][hapmap]
rs9758600	0.91[CEU][hapmap]
rs9823942	0.94[CEU][hapmap]
rs9828200	0.94[CEU][hapmap]
rs9832952	0.88[AMR][1000 genomes]
rs9837334	1.00[CEU][hapmap]
rs9838433	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9844581	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9850021	0.94[CEU][hapmap]
rs9857727	0.94[CEU][hapmap]
rs9859692	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9865532	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9868870	0.94[CEU][hapmap]
rs9869945	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9875961	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9877272	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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
rs6446245	HEMK1	cis	Lymphoblastoid	GTEx
rs6446245	HEMK1	cis	cerebellum	SCAN
rs6446245	NBEAL2	cis	cerebellum	SCAN
rs6446245	TNNC1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51033400-51037400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:51034600-51037400	Weak transcription	Liver	Liver

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