Variant report

Variant	rs1474790
Chromosome Location	chr6:81036745-81036746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 169 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:165)

rs_ID	r²[population]
rs1040592	0.94[AFR][1000 genomes]
rs1040594	0.92[AFR][1000 genomes]
rs1040595	0.92[AFR][1000 genomes]
rs1040596	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1042368	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10864	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1157978	0.91[AFR][1000 genomes]
rs1157979	0.91[AFR][1000 genomes]
rs1159505	0.89[AFR][1000 genomes]
rs1159506	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1179576	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs1179577	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs1184704	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11961389	0.81[JPT][hapmap]
rs11966170	0.80[AFR][1000 genomes]
rs1324119	0.80[JPT][hapmap]
rs15062	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1541208	0.92[AFR][1000 genomes]
rs1541209	0.90[AFR][1000 genomes]
rs1541210	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1541211	0.92[AFR][1000 genomes]
rs1546928	0.89[AFR][1000 genomes]
rs1546930	0.86[AFR][1000 genomes]
rs16891629	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1883974	0.89[AFR][1000 genomes]
rs1883975	0.91[AFR][1000 genomes]
rs1883976	0.91[AFR][1000 genomes]
rs1988589	0.92[AFR][1000 genomes]
rs2143885	0.87[AFR][1000 genomes]
rs2143886	0.91[AFR][1000 genomes]
rs2179839	0.91[AFR][1000 genomes]
rs2179840	0.91[AFR][1000 genomes]
rs2179841	0.91[AFR][1000 genomes]
rs2179843	0.91[AFR][1000 genomes]
rs2207142	0.91[AFR][1000 genomes]
rs2207143	0.92[AFR][1000 genomes]
rs2223874	0.91[AFR][1000 genomes]
rs2223876	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2322747	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs2322749	0.91[AFR][1000 genomes]
rs2322750	0.91[AFR][1000 genomes]
rs2322751	0.92[AFR][1000 genomes]
rs2322752	0.91[AFR][1000 genomes]
rs2322754	0.91[AFR][1000 genomes]
rs2322755	0.91[AFR][1000 genomes]
rs2322756	0.91[AFR][1000 genomes]
rs2322757	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2322758	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2322759	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2322760	0.89[AFR][1000 genomes]
rs2322761	0.91[AFR][1000 genomes]
rs2322762	0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs2322763	0.90[AFR][1000 genomes]
rs2874849	0.92[AFR][1000 genomes]
rs2874851	0.90[AFR][1000 genomes]
rs3792994	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs3805848	0.83[CHB][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs3805850	0.91[AFR][1000 genomes]
rs3805851	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs3805852	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3805856	0.91[AFR][1000 genomes]
rs3805896	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs3828745	0.80[AFR][1000 genomes]
rs3828746	0.88[AFR][1000 genomes]
rs4235811	0.89[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4235812	0.91[AFR][1000 genomes]
rs4502885	0.83[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs4613773	0.91[AFR][1000 genomes]
rs4706114	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4706115	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4706118	0.87[AFR][1000 genomes]
rs4706832	0.89[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4706833	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4706835	0.98[ASN][1000 genomes]
rs4706836	0.98[ASN][1000 genomes]
rs4706837	0.92[AFR][1000 genomes]
rs4706838	0.89[AFR][1000 genomes]
rs4706839	0.89[AFR][1000 genomes]
rs5003782	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs581860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs58780569	0.83[AFR][1000 genomes]
rs588186	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs59904615	0.82[AFR][1000 genomes]
rs606319	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs61198482	0.92[ASN][1000 genomes]
rs620176	0.97[ASN][1000 genomes]
rs632362	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs636361	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs636464	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs637323	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6454151	0.97[ASN][1000 genomes]
rs6454152	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs651314	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs652713	0.97[ASN][1000 genomes]
rs653141	0.97[ASN][1000 genomes]
rs653556	0.97[ASN][1000 genomes]
rs653581	0.97[ASN][1000 genomes]
rs653582	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs653596	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs653959	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs654435	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs660208	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs661018	0.97[ASN][1000 genomes]
rs662408	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs666032	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs668643	0.97[ASN][1000 genomes]
rs676213	0.97[ASN][1000 genomes]
rs676310	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs678079	0.97[ASN][1000 genomes]
rs689407	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6902457	0.99[ASN][1000 genomes]
rs6906534	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6907420	0.97[ASN][1000 genomes]
rs6907781	0.97[ASN][1000 genomes]
rs6921240	0.82[AFR][1000 genomes]
rs6921246	0.82[AFR][1000 genomes]
rs6921321	0.82[AFR][1000 genomes]
rs6927954	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6928305	0.97[ASN][1000 genomes]
rs6934902	0.97[ASN][1000 genomes]
rs700490	0.89[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs700491	0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs723307	0.89[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs723588	0.82[AFR][1000 genomes]
rs73463537	0.93[ASN][1000 genomes]
rs73467561	0.80[AFR][1000 genomes]
rs742834	0.80[JPT][hapmap]
rs7740932	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs7740958	0.83[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs7742132	0.91[AFR][1000 genomes]
rs7742286	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7742563	0.86[AFR][1000 genomes]
rs7747016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758761	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs7759304	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs7762655	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7767703	0.92[AFR][1000 genomes]
rs806840	0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs806843	0.89[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs806845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs809876	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926731	0.92[AFR][1000 genomes]
rs926732	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs926733	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs9343983	0.83[AFR][1000 genomes]
rs9350852	0.80[AFR][1000 genomes]
rs9352818	0.89[AFR][1000 genomes]
rs9352819	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9352820	0.83[AFR][1000 genomes]
rs9352821	0.83[AFR][1000 genomes]
rs9352823	0.83[AFR][1000 genomes]
rs9352824	0.80[AFR][1000 genomes]
rs9352825	0.82[AFR][1000 genomes]
rs9352827	0.82[AFR][1000 genomes]
rs9359414	0.83[AFR][1000 genomes]
rs9361594	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs9361602	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9361603	0.83[AFR][1000 genomes]
rs9361604	0.82[AFR][1000 genomes]
rs9443738	0.97[ASN][1000 genomes]
rs9443745	0.92[AFR][1000 genomes]
rs9448919	0.97[ASN][1000 genomes]
rs986438	1.00[YRI][hapmap];0.94[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034096	chr6:80856135-81150170	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv932996	chr6:80880896-81134991	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv497995	chr6:80883701-81134991	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1796319	chr6:81034505-81058025	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1474790	BCKDHB	cis	multi-tissue	Pritchard
rs1474790	BCKDHB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:81005200-81056200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:81015600-81037400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:81026800-81037400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:81027000-81044600	Weak transcription	Aorta	Aorta
5	chr6:81029400-81038200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:81029400-81038600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:81029400-81079600	Weak transcription	HSMM	muscle
8	chr6:81032000-81037600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:81033800-81070200	Weak transcription	Left Ventricle	heart
10	chr6:81034000-81039200	Weak transcription	Esophagus	oesophagus
11	chr6:81035200-81039200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:81035600-81037400	Weak transcription	Fetal Lung	lung
13	chr6:81035600-81037600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:81035800-81036800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:81035800-81037200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:81036200-81037400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:81036600-81041000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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