Variant report

Variant	rs3805913
Chromosome Location	chr6:80927322-80927323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10080237	0.87[MEX][hapmap]
rs10455370	0.87[MEX][hapmap]
rs10943698	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12209624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359239	0.89[CHB][hapmap]
rs1408292	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1535825	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs1575541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1892475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2179842	0.87[MEX][hapmap]
rs2256531	0.84[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap]
rs2298307	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs2322631	0.87[MEX][hapmap]
rs2322632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2322633	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.87[ASN][1000 genomes]
rs2322635	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2490232	0.82[MEX][hapmap]
rs2490234	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2490239	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2490241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2490244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2490245	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2490250	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2490251	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];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2490253	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2505927	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505929	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2505930	0.82[AMR][1000 genomes]
rs2505932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2505935	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505939	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505942	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505944	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805878	0.92[GIH][hapmap]
rs3805885	0.86[MEX][hapmap]
rs3805903	0.95[CHB][hapmap]
rs3805907	0.87[MEX][hapmap]
rs3805911	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256394	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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];0.85[ASN][1000 genomes]
rs4706834	0.87[MEX][hapmap]
rs583426	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs590641	0.81[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs613588	0.92[GIH][hapmap]
rs627240	0.90[MEX][hapmap]
rs638056	0.81[MEX][hapmap]
rs643987	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs648831	0.94[LWK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs660888	0.92[GIH][hapmap]
rs676311	0.92[GIH][hapmap]
rs682482	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs684251	0.95[CHB][hapmap];0.88[YRI][hapmap]
rs684283	0.95[CHB][hapmap];0.88[YRI][hapmap]
rs686556	0.81[ASN][1000 genomes]
rs688867	0.84[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6907729	0.87[MEX][hapmap]
rs6938280	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs742833	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741013	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7745301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7770383	0.82[ASN][1000 genomes]
rs7771645	1.00[YRI][hapmap]
rs806783	0.84[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.80[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9341806	1.00[YRI][hapmap]
rs9341808	0.83[ASN][1000 genomes]
rs9343974	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs9343977	0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap]
rs9350847	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs942381	1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs9448911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978814	0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
2	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
3	nsv886309	chr6:80880138-80959885	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv886310	chr6:80880138-81025879	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1033452	chr6:80888667-81000213	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	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
rs3805913	BCKDHB	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80882400-80935400	Weak transcription	Dnd41	blood
2	chr6:80891600-80931200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:80896400-80927400	Weak transcription	Aorta	Aorta
4	chr6:80896400-80943800	Weak transcription	Right Ventricle	heart
5	chr6:80908000-80936200	Weak transcription	Fetal Lung	lung
6	chr6:80909000-80940200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:80910000-80933400	Weak transcription	Esophagus	oesophagus
8	chr6:80911800-80935200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:80914600-80980400	Weak transcription	Ovary	ovary
10	chr6:80914800-80929000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:80914800-80934400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:80914800-80938400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr6:80914800-80938600	Weak transcription	Liver	Liver
14	chr6:80915400-80938200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:80915400-80942000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:80915800-80956000	Weak transcription	Brain Substantia Nigra	brain
17	chr6:80916800-80930000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:80920800-80929200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:80920800-80943600	Weak transcription	Psoas Muscle	Psoas
20	chr6:80920800-80953800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:80921200-80929000	Weak transcription	Left Ventricle	heart
22	chr6:80921200-80940200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:80921200-80940200	Weak transcription	HSMMtube	muscle
24	chr6:80921400-80929200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:80921400-80973200	Weak transcription	Primary B cells from cord blood	blood
26	chr6:80921600-80938400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:80922200-80964200	Weak transcription	Fetal Intestine Small	intestine
28	chr6:80922400-80929200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:80922600-80930000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:80924000-80928000	Weak transcription	Stomach Mucosa	stomach
31	chr6:80924000-80933400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:80924000-80938400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:80924000-80942800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:80924000-80968400	Weak transcription	Gastric	stomach
35	chr6:80924000-80976000	Weak transcription	HSMM	muscle
36	chr6:80924200-80927600	Weak transcription	Fetal Heart	heart
37	chr6:80924200-80938600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:80925200-80931800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:80925200-80933200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:80926800-80927400	Weak transcription	Fetal Stomach	stomach
41	chr6:80926800-80928000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:80927200-80927400	Enhancers	Colon Smooth Muscle	Colon
43	chr6:80927200-80927400	Active TSS	Stomach Smooth Muscle	stomach
44	chr6:80927200-80927400	Enhancers	NHDF-Ad	bronchial
45	chr6:80927200-80928000	Enhancers	Osteobl	bone
46	chr6:80927200-80928600	Enhancers	Rectal Smooth Muscle	rectum

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