Variant report

Variant	rs2179840
Chromosome Location	chr6:81048110-81048111
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:81047651..81048631-chr6:81237581..81238534,2	MCF-7	breast:
2	chr6:81047941..81048548-chr6:82463318..82463845,3	K562	blood:
3	chr6:81047806..81048624-chr6:81314824..81315362,2	MCF-7	breast:
4	chr6:81047988..81048553-chr6:81186140..81186935,2	MCF-7	breast:
5	chr6:81047724..81048347-chr6:82463313..82464141,2	MCF-7	breast:

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1040592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1040594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1040595	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1040596	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1042367	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1042368	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10864	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1157978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1157979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1159503	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1159505	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1159506	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11961331	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11966170	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1320614	0.83[AFR][1000 genomes]
rs1320615	0.83[AFR][1000 genomes]
rs1320616	0.83[AFR][1000 genomes]
rs1474790	0.91[AFR][1000 genomes]
rs15062	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1541208	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541209	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541210	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541211	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1546928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1546930	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1811844	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1883974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1883976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1988589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2143885	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2143886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2179839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2207142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2207143	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2223874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223876	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2322749	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2322750	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2322751	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2322752	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2322754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2322755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2322756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2322757	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2322758	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2322759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2322760	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2322761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2322762	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2322763	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2874849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2874851	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34758321	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3792994	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805848	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3805850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805852	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3828745	0.89[AFR][1000 genomes]
rs3828746	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4134487	0.81[AFR][1000 genomes]
rs4235812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4502885	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4613773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4706114	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4706115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4706118	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4706837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4706838	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4706839	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5003782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58780569	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs59904615	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6454152	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6921240	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6921246	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6921321	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs700491	0.82[AFR][1000 genomes]
rs723588	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs73467561	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73467566	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73467567	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73467571	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73467576	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7740932	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7740958	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7742132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7742563	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7745921	0.84[AFR][1000 genomes]
rs7747016	0.85[AFR][1000 genomes]
rs7758761	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7759304	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7762655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7766087	0.83[AFR][1000 genomes]
rs7766633	0.83[AFR][1000 genomes]
rs7767703	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs806845	0.87[AFR][1000 genomes]
rs806847	0.86[AFR][1000 genomes]
rs806848	0.88[AFR][1000 genomes]
rs926731	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs926732	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs926733	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9341812	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9343983	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9350849	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9350852	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9350853	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9352818	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9352819	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9352820	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9352821	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9352823	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9352824	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9352825	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9352827	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9359414	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9361602	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9361603	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9361604	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9361605	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9361607	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9443745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs986438	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
5	esv16646	chr6:81040322-81055387	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv531333	chr6:81042427-81836484	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv463907	chr6:81047559-81075912	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv604053	chr6:81047559-81075912	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2179840	BCKDHB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 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	chr6:81029400-81079600	Weak transcription	HSMM	muscle
3	chr6:81033800-81070200	Weak transcription	Left Ventricle	heart
4	chr6:81042200-81056400	Weak transcription	Fetal Heart	heart
5	chr6:81044400-81050200	Weak transcription	Fetal Kidney	kidney
6	chr6:81045200-81051000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:81045600-81051200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:81045800-81052600	Weak transcription	Osteobl	bone
9	chr6:81046600-81050400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:81046800-81051400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:81047000-81051200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:81047200-81048200	Weak transcription	HUVEC	blood vessel
13	chr6:81047200-81048400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr6:81047600-81048400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr6:81047600-81048600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr6:81047600-81048600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:81047800-81048400	Enhancers	Liver	Liver
18	chr6:81047800-81048600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr6:81048000-81048200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:81048000-81048200	Flanking Active TSS	Aorta	Aorta
21	chr6:81048000-81048200	Enhancers	Fetal Brain Female	brain
22	chr6:81048000-81048200	Enhancers	Fetal Stomach	stomach
23	chr6:81048000-81048200	Enhancers	Pancreas	Pancrea
24	chr6:81048000-81048200	Enhancers	Psoas Muscle	Psoas
25	chr6:81048000-81048400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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