Variant report

Variant	rs6109850
Chromosome Location	chr20:13368946-13368947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs12329620	0.82[AMR][1000 genomes]
rs1812562	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2145139	0.89[AMR][1000 genomes]
rs2327755	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs28867078	0.83[EUR][1000 genomes]
rs45489891	0.96[EUR][1000 genomes]
rs45602236	0.96[EUR][1000 genomes]
rs55940819	1.00[EUR][1000 genomes]
rs57675086	0.89[AMR][1000 genomes]
rs58023165	0.82[AMR][1000 genomes]
rs59388287	0.82[AMR][1000 genomes]
rs6033689	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6033690	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6033693	0.89[AMR][1000 genomes]
rs6033694	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs6033695	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs6033714	0.82[AMR][1000 genomes]
rs6033716	0.82[AMR][1000 genomes]
rs6033718	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6042061	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042063	0.82[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042068	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042069	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6042075	0.89[AMR][1000 genomes]
rs6042076	0.82[CEU][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6042077	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs6042079	0.89[AMR][1000 genomes]
rs6042080	0.82[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6042093	0.82[CEU][hapmap]
rs6042095	0.82[AMR][1000 genomes]
rs6042101	0.82[AMR][1000 genomes]
rs6042105	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6042107	0.82[AMR][1000 genomes]
rs6042108	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6042111	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6042116	0.82[AMR][1000 genomes]
rs6042120	0.82[AMR][1000 genomes]
rs6042123	0.82[AMR][1000 genomes]
rs6042130	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6042136	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6042142	0.82[AMR][1000 genomes]
rs6042145	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6042151	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6042154	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6105082	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6105083	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6105088	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs6105089	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs6105091	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6105095	0.82[AMR][1000 genomes]
rs6105097	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6105105	0.82[AMR][1000 genomes]
rs6105108	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6105109	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6109848	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6109849	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6109859	0.89[AMR][1000 genomes]
rs6109863	0.83[YRI][hapmap];0.89[AMR][1000 genomes]
rs6109867	0.82[AMR][1000 genomes]
rs6109868	0.82[CEU][hapmap]
rs6109879	0.82[AMR][1000 genomes]
rs6109882	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6109883	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6109885	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6109889	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6109895	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs6109896	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs6109900	0.82[AMR][1000 genomes]
rs6109901	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs61518689	0.82[AMR][1000 genomes]
rs7274078	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs7348566	0.82[AMR][1000 genomes]
rs8119260	0.82[AMR][1000 genomes]
rs8121784	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9653627	0.82[CEU][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13361800-13369400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr20:13362400-13370600	Weak transcription	HepG2	liver
3	chr20:13362600-13374000	Weak transcription	Fetal Lung	lung
4	chr20:13362600-13376800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr20:13362800-13380600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr20:13363200-13377400	Weak transcription	Fetal Brain Female	brain
7	chr20:13363400-13373200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr20:13363600-13375800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr20:13363600-13375800	Weak transcription	HSMMtube	muscle
10	chr20:13363800-13373400	Weak transcription	Liver	Liver
11	chr20:13363800-13376200	Weak transcription	Fetal Muscle Leg	muscle
12	chr20:13364000-13377400	Weak transcription	Brain Angular Gyrus	brain
13	chr20:13364400-13370800	Weak transcription	Fetal Intestine Small	intestine
14	chr20:13364400-13371000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr20:13364400-13376400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr20:13364400-13415400	Weak transcription	Right Ventricle	heart
17	chr20:13364600-13371800	Strong transcription	Primary T cells from cord blood	blood
18	chr20:13364600-13374200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr20:13364600-13379000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr20:13364600-13416800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr20:13364800-13375400	Weak transcription	Colonic Mucosa	Colon
22	chr20:13364800-13377600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr20:13365400-13373000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr20:13365400-13375800	Weak transcription	HSMM	muscle
25	chr20:13365600-13369400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr20:13365600-13370400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr20:13365600-13376000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr20:13366200-13370800	Weak transcription	Lung	lung
29	chr20:13366200-13373600	Weak transcription	Brain Hippocampus Middle	brain
30	chr20:13366200-13373800	Weak transcription	Esophagus	oesophagus
31	chr20:13366600-13370600	Weak transcription	Gastric	stomach
32	chr20:13366600-13375600	Weak transcription	Fetal Intestine Large	intestine
33	chr20:13366800-13370600	Weak transcription	Adipose Nuclei	Adipose
34	chr20:13366800-13375800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr20:13367000-13370600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr20:13367000-13370800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr20:13367200-13378400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr20:13367400-13369800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr20:13367600-13369600	Strong transcription	Fetal Thymus	thymus
40	chr20:13367600-13372000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr20:13367600-13373800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr20:13368000-13372200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr20:13368000-13376600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr20:13368200-13369400	Strong transcription	Primary B cells from cord blood	blood
45	chr20:13368200-13369400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr20:13368200-13369600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr20:13368200-13370000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr20:13368200-13371800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr20:13368200-13372000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr20:13368400-13369000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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