Variant report

Variant	rs6459163
Chromosome Location	chr6:56353760-56353761
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs11751569	0.82[YRI][hapmap]
rs11753813	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11757910	0.80[YRI][hapmap]
rs11757941	0.82[YRI][hapmap]
rs11758339	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11759493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11961668	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12174955	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12527139	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13204556	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13218268	0.82[YRI][hapmap]
rs1359068	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359070	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535610	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535612	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1570492	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2273972	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2273973	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294697	0.82[YRI][hapmap]
rs2397221	0.82[YRI][hapmap]
rs2397226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2894837	0.88[CHB][hapmap]
rs34954984	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35671304	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35926142	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3927453	0.91[ASN][1000 genomes]
rs4130060	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4143828	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4236139	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs4236140	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs4236141	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4236142	0.80[ASN][1000 genomes]
rs4236143	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4236144	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4236145	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs4283892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4331988	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4346846	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs4454141	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs4466244	0.80[ASN][1000 genomes]
rs4499917	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4544910	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45486696	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4712132	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs4712133	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs4715625	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]
rs4715626	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs4715627	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs4715628	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4715629	0.87[CEU][hapmap]
rs4715630	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59101638	0.86[ASN][1000 genomes]
rs595238	0.91[YRI][hapmap]
rs636389	0.91[YRI][hapmap]
rs6459161	0.86[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs656988	0.88[CHB][hapmap]
rs6904202	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs6906792	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs6907917	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6911502	0.82[CHB][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs6913572	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914325	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6922770	0.83[CEU][hapmap]
rs6927258	0.87[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6928601	0.87[ASN][1000 genomes]
rs6939305	0.86[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs721475	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72877350	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7741295	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7746753	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755220	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7755361	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs7755573	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7758054	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7759875	0.85[CEU][hapmap]
rs7760640	0.82[CEU][hapmap]
rs7760695	0.81[EUR][1000 genomes]
rs7761281	0.90[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap]
rs7762629	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7775847	0.82[YRI][hapmap]
rs9296848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296850	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9349822	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9349823	0.90[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9349824	0.87[ASN][1000 genomes]
rs9349825	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9349828	0.86[JPT][hapmap]
rs9357921	0.83[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9357922	0.86[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9370531	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9370533	0.90[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap]
rs9370534	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9370535	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382631	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9382635	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396211	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9396213	0.82[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs9396214	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9396215	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9396218	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464389	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9475709	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9475713	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs9475714	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs9475716	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56308800-56373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:56315600-56371000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:56328600-56362000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:56329200-56373800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:56330000-56372400	Weak transcription	Lung	lung
6	chr6:56330200-56357400	Weak transcription	Esophagus	oesophagus
7	chr6:56334400-56359400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:56337600-56364600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:56337600-56376000	Weak transcription	Gastric	stomach
10	chr6:56339800-56354400	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:56339800-56355800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:56341800-56407400	Weak transcription	Spleen	Spleen
13	chr6:56344200-56371600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:56344600-56354200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:56344800-56354400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:56344800-56362000	Strong transcription	Fetal Lung	lung
17	chr6:56344800-56372200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:56345000-56384200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:56345600-56356800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:56345800-56362000	Weak transcription	Colonic Mucosa	Colon
21	chr6:56346000-56372400	Weak transcription	Psoas Muscle	Psoas
22	chr6:56347000-56362000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:56347600-56355600	Weak transcription	NHEK	skin
24	chr6:56347600-56362200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:56347600-56372200	Weak transcription	Right Ventricle	heart
26	chr6:56347800-56362000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:56348200-56371000	Weak transcription	Small Intestine	intestine
28	chr6:56348200-56373400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr6:56348400-56355800	Weak transcription	Fetal Heart	heart
30	chr6:56348600-56374600	Strong transcription	Fetal Intestine Large	intestine
31	chr6:56348800-56373400	Weak transcription	Stomach Mucosa	stomach
32	chr6:56349400-56354400	Strong transcription	Adipose Nuclei	Adipose
33	chr6:56349400-56354600	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:56349600-56359200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr6:56349600-56364200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr6:56350000-56354200	Strong transcription	HSMMtube	muscle
37	chr6:56350200-56354400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:56350200-56356400	Strong transcription	HSMM	muscle
39	chr6:56350200-56367000	Strong transcription	Liver	Liver
40	chr6:56350400-56354400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr6:56350400-56354800	Strong transcription	Colon Smooth Muscle	Colon
42	chr6:56350400-56355800	Weak transcription	Hela-S3	cervix
43	chr6:56350400-56356000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:56350400-56356200	Strong transcription	NHDF-Ad	bronchial
45	chr6:56350400-56370800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:56350600-56354000	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:56350800-56355200	Strong transcription	Brain Anterior Caudate	brain
48	chr6:56350800-56355600	Strong transcription	Osteobl	bone
49	chr6:56351200-56354200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:56351200-56354400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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