Variant report

Variant	rs6039969
Chromosome Location	chr20:1099903-1099904
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1099609..1102022-chr20:1115738..1118219,2	K562	blood:
2	chr20:1099357..1100931-chr20:1102003..1104319,2	K562	blood:
3	chr20:1099416..1102293-chr20:1159326..1161396,2	K562	blood:
4	chr20:1099167..1103189-chr20:1144544..1147545,4	K562	blood:
5	chr11:62609153..62610033-chr20:1099017..1099920,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction
ENSG00000125818	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1018408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1033664	0.89[EUR][1000 genomes]
rs2317425	0.89[EUR][1000 genomes]
rs2317428	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4344980	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4813939	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4813940	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6039664	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6039734	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6039867	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6039902	1.00[EUR][1000 genomes]
rs6039903	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6040022	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6040031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6057111	0.89[EUR][1000 genomes]
rs6057117	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6057127	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6077895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6077896	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6087132	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531450	chr20:809607-1221836	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1065838	chr20:866302-1147601	Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544139	chr20:866302-1147601	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1055328	chr20:867911-1145765	Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1059611	chr20:867911-1158694	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv544140	chr20:867911-1158694	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv949356	chr20:961527-1135413	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912585	chr20:992713-1210647	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	esv1799982	chr20:1097289-1136252	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1098200-1100000	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr20:1098400-1100000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:1098400-1100000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr20:1098400-1100000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr20:1098400-1100000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr20:1098400-1100000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:1098400-1100200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr20:1098400-1100400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr20:1098400-1101000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr20:1098600-1100000	Active TSS	Left Ventricle	heart
11	chr20:1098600-1100000	Active TSS	Ovary	ovary
12	chr20:1098600-1100000	Active TSS	Pancreas	Pancrea
13	chr20:1098600-1100000	Active TSS	Placenta Amnion	Placenta Amnion
14	chr20:1098600-1100000	Active TSS	Psoas Muscle	Psoas
15	chr20:1098600-1100200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr20:1098600-1100200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr20:1098600-1100200	Active TSS	Right Atrium	heart
18	chr20:1098600-1100400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr20:1098600-1100400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr20:1098600-1100600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr20:1098800-1100000	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr20:1098800-1100000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr20:1098800-1100000	Active TSS	Colon Smooth Muscle	Colon
24	chr20:1098800-1100000	Active TSS	Fetal Intestine Large	intestine
25	chr20:1098800-1100000	Active TSS	Gastric	stomach
26	chr20:1098800-1100000	Active TSS	Lung	lung
27	chr20:1098800-1100000	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr20:1098800-1100000	Active TSS	NHLF	lung
29	chr20:1098800-1100200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr20:1098800-1100200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr20:1098800-1100200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr20:1098800-1100200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr20:1098800-1100200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr20:1098800-1100200	Active TSS	Aorta	Aorta
35	chr20:1098800-1100200	Active TSS	Fetal Intestine Small	intestine
36	chr20:1098800-1100200	Active TSS	Small Intestine	intestine
37	chr20:1098800-1100400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr20:1098800-1100400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr20:1098800-1100400	Active TSS	A549	lung
40	chr20:1099000-1100000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr20:1099000-1100000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr20:1099000-1100000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr20:1099000-1100000	Active TSS	Stomach Mucosa	stomach
44	chr20:1099000-1100000	Active TSS	HMEC	breast
45	chr20:1099000-1100000	Active TSS	NHDF-Ad	bronchial
46	chr20:1099000-1100200	Active TSS	H9 Cell Line	embryonic stem cell
47	chr20:1099000-1100200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr20:1099000-1100200	Active TSS	Fetal Kidney	kidney
49	chr20:1099000-1100200	Active TSS	GM12878-XiMat	blood
50	chr20:1099000-1100200	Bivalent/Poised TSS	HepG2	liver

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