Variant report

Variant	rs6134879
Chromosome Location	chr20:13464524-13464525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs13039162	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13042843	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070305	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070334	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2073324	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2103972	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2182708	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2208207	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2208208	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273480	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747931	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789342	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789347	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789348	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789349	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4813131	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4814236	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4814238	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4814242	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57218913	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042106	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6042128	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6042153	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042225	0.81[AFR][1000 genomes]
rs6074611	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6074612	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6074613	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6074618	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6074627	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6079066	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6079072	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079074	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079075	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079077	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079085	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6079095	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6079106	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6105096	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6105098	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6105103	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6105113	0.96[ASN][1000 genomes]
rs6109887	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6109891	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109903	0.90[ASN][1000 genomes]
rs6109905	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109958	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6131483	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6131485	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6131488	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6134902	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134912	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73086013	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062049	chr20:13347580-13477455	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv544186	chr20:13347580-13477455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv585435	chr20:13410638-13582476	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking 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	4 gene(s)	inside rSNPs	diseases
7	nsv458871	chr20:13447896-13573415	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv585436	chr20:13447896-13573415	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13395600-13477800	Weak transcription	Gastric	stomach
2	chr20:13430000-13467800	Weak transcription	Ovary	ovary
3	chr20:13430200-13467800	Weak transcription	Pancreas	Pancrea
4	chr20:13442600-13471600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr20:13442800-13467800	Weak transcription	Aorta	Aorta
6	chr20:13445400-13467800	Weak transcription	Fetal Stomach	stomach
7	chr20:13454400-13471200	Weak transcription	Small Intestine	intestine
8	chr20:13457000-13471400	Weak transcription	Hela-S3	cervix
9	chr20:13457800-13466000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr20:13458000-13470600	Weak transcription	Colon Smooth Muscle	Colon
11	chr20:13458000-13471600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:13458600-13472600	Weak transcription	Psoas Muscle	Psoas
13	chr20:13459400-13472000	Weak transcription	HSMMtube	muscle
14	chr20:13459600-13469800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr20:13459600-13472600	Weak transcription	NH-A	brain
16	chr20:13459800-13465800	Weak transcription	Spleen	Spleen
17	chr20:13460200-13471600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr20:13460600-13469800	Weak transcription	Fetal Brain Female	brain
19	chr20:13460600-13472600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr20:13460800-13472000	Weak transcription	Brain Hippocampus Middle	brain
21	chr20:13460800-13472000	Weak transcription	NHEK	skin
22	chr20:13461000-13465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr20:13461400-13472000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr20:13461800-13472000	Weak transcription	NHDF-Ad	bronchial
25	chr20:13462200-13471800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr20:13462200-13477800	Weak transcription	Thymus	Thymus
27	chr20:13463000-13468600	Weak transcription	Fetal Brain Male	brain
28	chr20:13463400-13471400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr20:13463400-13480200	Weak transcription	Brain Angular Gyrus	brain
30	chr20:13463600-13471600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:13463800-13465200	Strong transcription	Primary T cells from cord blood	blood
32	chr20:13463800-13467200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr20:13463800-13467400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr20:13463800-13468000	Weak transcription	HepG2	liver
35	chr20:13463800-13471400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr20:13463800-13472000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:13463800-13481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr20:13464000-13464800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr20:13464000-13465600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr20:13464000-13466000	Weak transcription	Brain Anterior Caudate	brain
42	chr20:13464000-13466600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr20:13464000-13466800	Weak transcription	Placenta	Placenta
44	chr20:13464000-13467600	Weak transcription	Liver	Liver
45	chr20:13464000-13467800	Weak transcription	Fetal Lung	lung
46	chr20:13464000-13469400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr20:13464000-13469600	Weak transcription	Fetal Intestine Large	intestine
48	chr20:13464000-13469800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr20:13464000-13471600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr20:13464000-13472000	Weak transcription	Adipose Nuclei	Adipose

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