Variant report

Variant	rs6040022
Chromosome Location	chr20:1106944-1106945
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1102002..1104790-chr20:1105362..1109847,4	MCF-7	breast:
2	chr20:1106806..1108525-chr20:1110741..1113605,2	K562	blood:
3	chr20:1098147..1101828-chr20:1104480..1108337,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125818	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1018408	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2317428	1.00[AMR][1000 genomes]
rs4344980	1.00[AMR][1000 genomes]
rs4813939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4813940	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6039664	1.00[AMR][1000 genomes]
rs6039734	1.00[AMR][1000 genomes]
rs6039867	1.00[AMR][1000 genomes]
rs6039903	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6039969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6040031	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6057117	1.00[AMR][1000 genomes]
rs6057127	1.00[AMR][1000 genomes]
rs6077895	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6077896	1.00[AMR][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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1100400-1115200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:1100400-1132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr20:1100400-1146600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr20:1100800-1122200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr20:1101800-1111600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:1102200-1107600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr20:1102200-1128600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr20:1102600-1111200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr20:1102800-1113800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr20:1103600-1109000	Weak transcription	Fetal Brain Male	brain
11	chr20:1103600-1111600	Strong transcription	Primary B cells from cord blood	blood
12	chr20:1103600-1112600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr20:1103600-1113800	Strong transcription	Placenta	Placenta
14	chr20:1103600-1114000	Strong transcription	Fetal Thymus	thymus
15	chr20:1103600-1127800	Weak transcription	Fetal Heart	heart
16	chr20:1103600-1130800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr20:1103600-1130800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr20:1103800-1111400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr20:1103800-1112400	Strong transcription	NHEK	skin
20	chr20:1104000-1109200	Strong transcription	Primary hematopoietic stem cells	blood
21	chr20:1104000-1111000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr20:1104000-1112600	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr20:1104000-1113800	Strong transcription	Primary T cells from cord blood	blood
24	chr20:1104000-1113800	Strong transcription	A549	lung
25	chr20:1104000-1114000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr20:1104200-1113000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr20:1104200-1122400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr20:1104200-1122600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr20:1104400-1108600	Weak transcription	Stomach Mucosa	stomach
30	chr20:1104400-1108600	Strong transcription	Hela-S3	cervix
31	chr20:1104600-1107600	Weak transcription	Small Intestine	intestine
32	chr20:1104600-1111600	Strong transcription	HUVEC	blood vessel
33	chr20:1104600-1112800	Strong transcription	HMEC	breast
34	chr20:1104600-1115200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr20:1104600-1125600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr20:1104600-1128600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr20:1104600-1135800	Strong transcription	Dnd41	blood
38	chr20:1105200-1107600	Weak transcription	Psoas Muscle	Psoas
39	chr20:1105200-1112200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr20:1105200-1112600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr20:1105200-1114000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr20:1105200-1121600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr20:1105400-1107600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr20:1105400-1108600	Strong transcription	GM12878-XiMat	blood
45	chr20:1105400-1109000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr20:1105400-1111200	Strong transcription	NHDF-Ad	bronchial
47	chr20:1105400-1112800	Strong transcription	Fetal Intestine Large	intestine
48	chr20:1105400-1113000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr20:1105400-1113000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr20:1105400-1113200	Strong transcription	HepG2	liver

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