Variant report

Variant	rs6109908
Chromosome Location	chr20:13465902-13465903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11698396	0.81[ASN][1000 genomes]
rs11698691	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12329562	0.95[ASN][1000 genomes]
rs13041649	0.81[ASN][1000 genomes]
rs2073323	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2327789	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28444692	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2876356	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789343	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789344	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789345	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789350	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4411781	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033720	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033723	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033727	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033731	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033733	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033735	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033736	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033737	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033741	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033745	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033755	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042156	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042167	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042174	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042176	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042179	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042181	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042183	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042184	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042186	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042212	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6105115	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105116	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109906	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109913	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109915	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109920	0.80[ASN][1000 genomes]
rs6131478	0.96[ASN][1000 genomes]
rs6131480	0.96[ASN][1000 genomes]
rs6131481	0.96[ASN][1000 genomes]
rs6131482	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134872	0.85[ASN][1000 genomes]
rs6134882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134885	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134890	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134892	0.94[ASN][1000 genomes]
rs6134893	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134894	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6134896	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134897	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134899	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134904	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134907	0.86[ASN][1000 genomes]
rs6134908	0.86[ASN][1000 genomes]
rs6134909	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6134911	0.81[ASN][1000 genomes]
rs6134913	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6134914	0.81[ASN][1000 genomes]
rs6134915	0.81[ASN][1000 genomes]
rs73080067	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73080080	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73086022	0.81[ASN][1000 genomes]
rs73086039	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8115098	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8123095	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8126063	0.94[ASN][1000 genomes]
rs8184309	0.81[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:78 , 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	chr20:13460200-13471600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr20:13460600-13469800	Weak transcription	Fetal Brain Female	brain
18	chr20:13460600-13472600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr20:13460800-13472000	Weak transcription	Brain Hippocampus Middle	brain
20	chr20:13460800-13472000	Weak transcription	NHEK	skin
21	chr20:13461400-13472000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr20:13461800-13472000	Weak transcription	NHDF-Ad	bronchial
23	chr20:13462200-13471800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr20:13462200-13477800	Weak transcription	Thymus	Thymus
25	chr20:13463000-13468600	Weak transcription	Fetal Brain Male	brain
26	chr20:13463400-13471400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr20:13463400-13480200	Weak transcription	Brain Angular Gyrus	brain
28	chr20:13463600-13471600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr20:13463800-13467200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr20:13463800-13467400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr20:13463800-13468000	Weak transcription	HepG2	liver
32	chr20:13463800-13471400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr20:13463800-13472000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr20:13463800-13481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr20:13464000-13466000	Weak transcription	Brain Anterior Caudate	brain
37	chr20:13464000-13466600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr20:13464000-13466800	Weak transcription	Placenta	Placenta
39	chr20:13464000-13467600	Weak transcription	Liver	Liver
40	chr20:13464000-13467800	Weak transcription	Fetal Lung	lung
41	chr20:13464000-13469400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr20:13464000-13469600	Weak transcription	Fetal Intestine Large	intestine
43	chr20:13464000-13469800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr20:13464000-13471600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr20:13464000-13472000	Weak transcription	Adipose Nuclei	Adipose
46	chr20:13464000-13472400	Weak transcription	A549	lung
47	chr20:13464000-13473800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr20:13464000-13473800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr20:13464000-13474800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr20:13464000-13475200	Weak transcription	Fetal Kidney	kidney

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