Variant report

Variant	rs2505939
Chromosome Location	chr6:80847817-80847818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10080237	0.87[MEX][hapmap]
rs10455370	0.87[MEX][hapmap]
rs10943698	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12209624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1359239	0.90[CHB][hapmap]
rs1408292	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535825	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1575541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1892475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179842	0.87[MEX][hapmap]
rs2256531	0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs2298307	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs2322628	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2322631	0.87[MEX][hapmap]
rs2322632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2322633	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[ASN][1000 genomes]
rs2322635	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2476826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2490232	0.82[MEX][hapmap]
rs2490234	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2490239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2490241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2490245	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2490250	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2490251	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2490253	0.82[EUR][1000 genomes]
rs2505927	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2505929	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505930	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2505932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2505935	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505942	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505944	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3805878	0.92[GIH][hapmap]
rs3805885	0.87[MEX][hapmap]
rs3805903	0.95[CHB][hapmap]
rs3805907	0.87[MEX][hapmap]
rs3805911	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3805913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3805919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812121	0.91[MEX][hapmap]
rs3812126	0.87[MEX][hapmap]
rs3828753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4256394	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4437429	0.87[MEX][hapmap]
rs4706113	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[ASN][1000 genomes]
rs4706834	0.87[MEX][hapmap]
rs583426	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs590641	0.81[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap]
rs613588	0.92[GIH][hapmap]
rs627240	0.91[MEX][hapmap]
rs638056	0.82[MEX][hapmap]
rs643987	0.82[ASN][1000 genomes]
rs660888	0.92[GIH][hapmap]
rs676311	0.92[GIH][hapmap]
rs684251	0.95[CHB][hapmap]
rs684283	0.95[CHB][hapmap]
rs688867	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs6907729	0.87[MEX][hapmap]
rs6938280	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs742833	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7741013	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7745301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7745545	0.81[ASN][1000 genomes]
rs7746917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs806783	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs806851	0.92[GIH][hapmap]
rs9294171	0.87[MEX][hapmap]
rs9294172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9343974	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs9343977	0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap]
rs9350847	0.85[CEU][hapmap]
rs942381	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs9448911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs978814	0.87[MEX][hapmap]

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	nsv830708	chr6:80844283-80996876	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2505939	BCKDHB	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80817000-80852800	Weak transcription	Psoas Muscle	Psoas
2	chr6:80818000-80861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:80818000-80866000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr6:80829400-80852000	Weak transcription	Fetal Stomach	stomach
5	chr6:80836200-80852800	Weak transcription	Right Ventricle	heart
6	chr6:80836400-80855800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:80836400-80863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:80836400-80891200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:80836600-80852800	Weak transcription	Pancreas	Pancrea
10	chr6:80837000-80852600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:80837000-80853000	Weak transcription	Fetal Kidney	kidney
12	chr6:80837000-80895200	Weak transcription	Fetal Intestine Small	intestine
13	chr6:80837400-80854200	Weak transcription	Brain Substantia Nigra	brain
14	chr6:80837600-80853000	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:80838400-80852800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:80838400-80853400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:80838600-80852800	Weak transcription	Aorta	Aorta
18	chr6:80838600-80857400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:80838600-80873200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:80838800-80852000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:80838800-80852000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:80838800-80852000	Weak transcription	NHDF-Ad	bronchial
23	chr6:80838800-80852200	Weak transcription	NH-A	brain
24	chr6:80838800-80852400	Weak transcription	HSMMtube	muscle
25	chr6:80838800-80852600	Weak transcription	NHLF	lung
26	chr6:80838800-80853200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:80839200-80873200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:80839200-80889600	Weak transcription	Lung	lung
29	chr6:80839600-80852800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:80839600-80857600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:80839600-80859600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:80840000-80852000	Weak transcription	Fetal Lung	lung
33	chr6:80840000-80860800	Weak transcription	Fetal Intestine Large	intestine
34	chr6:80840200-80855000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr6:80841000-80852400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr6:80841000-80852800	Weak transcription	Colonic Mucosa	Colon
37	chr6:80841000-80859200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:80841000-80860800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:80841200-80852000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:80841200-80852000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:80841200-80852800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:80841200-80852800	Weak transcription	HMEC	breast
43	chr6:80841200-80853200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:80841200-80854600	Weak transcription	Ovary	ovary
45	chr6:80841200-80855600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:80841200-80861400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:80841200-80895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:80841400-80853000	Weak transcription	Adipose Nuclei	Adipose
49	chr6:80841400-80873400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr6:80842200-80852800	Weak transcription	Fetal Muscle Leg	muscle

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