Variant report

Variant	rs6109891
Chromosome Location	chr20:13431042-13431043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs13039162	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13042843	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2057258	0.81[ASN][1000 genomes]
rs2070305	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070334	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2073324	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2103972	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2182708	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2208207	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208208	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273480	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747931	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3789342	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789347	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789348	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789349	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4813131	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4814236	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4814238	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4814242	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57218913	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6042106	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6042128	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042153	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042225	0.81[AFR][1000 genomes]
rs6074611	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6074612	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6074613	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6074618	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6074627	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6079066	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079072	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6079074	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079075	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6079077	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6079085	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079095	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6079106	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6105096	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6105098	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6105103	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6105113	0.93[ASN][1000 genomes]
rs6109887	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6109903	0.89[ASN][1000 genomes]
rs6109905	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109958	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6131483	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6131485	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6131488	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6134879	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134902	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134912	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73086013	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv21228	chr20:13283535-13447810	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv520595	chr20:13421045-13447896	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	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
9	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

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13379200-13463000	Weak transcription	HSMM	muscle
2	chr20:13395600-13477800	Weak transcription	Gastric	stomach
3	chr20:13403800-13435000	Weak transcription	HMEC	breast
4	chr20:13404400-13434800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:13404400-13434800	Weak transcription	NHEK	skin
6	chr20:13411400-13435000	Weak transcription	Lung	lung
7	chr20:13413600-13433400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr20:13415400-13435000	Weak transcription	Placenta	Placenta
9	chr20:13415600-13433600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr20:13416000-13438200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr20:13416200-13435000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr20:13416200-13436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr20:13416400-13434600	Weak transcription	Fetal Thymus	thymus
14	chr20:13420800-13444400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr20:13421800-13432800	Weak transcription	Psoas Muscle	Psoas
16	chr20:13421800-13436600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr20:13421800-13450000	Weak transcription	Fetal Lung	lung
18	chr20:13422000-13460400	Weak transcription	Primary B cells from cord blood	blood
19	chr20:13422000-13461200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr20:13422200-13435000	Weak transcription	Aorta	Aorta
21	chr20:13422400-13432000	Weak transcription	Primary T cells from cord blood	blood
22	chr20:13422400-13435200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr20:13423200-13433800	Weak transcription	K562	blood
24	chr20:13423800-13431800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:13424600-13435000	Weak transcription	Fetal Muscle Leg	muscle
26	chr20:13428200-13433600	Weak transcription	Small Intestine	intestine
27	chr20:13428200-13434600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr20:13428400-13432800	Weak transcription	HepG2	liver
29	chr20:13428400-13433800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr20:13428400-13448800	Weak transcription	Thymus	Thymus
31	chr20:13429600-13431800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr20:13429800-13437000	Strong transcription	Dnd41	blood
33	chr20:13430000-13467800	Weak transcription	Ovary	ovary
34	chr20:13430200-13433800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr20:13430200-13467800	Weak transcription	Pancreas	Pancrea
36	chr20:13430400-13431200	Enhancers	A549	lung
37	chr20:13430400-13442200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr20:13430600-13435400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:13430600-13436000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr20:13430800-13431400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr20:13430800-13431400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr20:13430800-13431600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr20:13430800-13433400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr20:13431000-13432600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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