Variant report

Variant	rs74173671
Chromosome Location	chr20:25226899-25226900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25226639-25227152	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr20:25226835-25229543	A549	lung:	n/a	n/a
3	CUX1	chr20:25226780-25227321	GM12878	blood:	n/a	chr20:25227154-25227168 chr20:25227160-25227169
4	POLR2A	chr20:25226530-25230405	PANC-1	pancreas:	n/a	n/a
5	JUN	chr20:25226856-25227056	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25226304..25227809-chr20:25275139..25278038,2	MCF-7	breast:
2	chr20:25057289..25058975-chr20:25226619..25228863,2	MCF-7	breast:
3	chr20:25174902..25179249-chr20:25225017..25231959,9	MCF-7	breast:
4	chr20:25202506..25206898-chr20:25226343..25231297,7	MCF-7	breast:
5	chr20:25174010..25179528-chr20:25225802..25231331,13	MCF-7	breast:

Variant related genes	Relation type
PYGB	TF binding region
ENSG00000197586	Chromatin interaction
ENSG00000100987	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13039195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34400168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35427265	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6083780	1.00[AFR][1000 genomes]
rs71337908	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs74173675	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription 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	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv828708	chr20:25223895-25231601	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25217600-25227600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr20:25219000-25227400	Weak transcription	Colon Smooth Muscle	Colon
3	chr20:25219400-25227600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr20:25219400-25228000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr20:25219600-25227000	Weak transcription	NHDF-Ad	bronchial
6	chr20:25219800-25227400	Weak transcription	NHLF	lung
7	chr20:25220200-25227000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr20:25220400-25227400	Weak transcription	Esophagus	oesophagus
9	chr20:25220600-25227200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr20:25222000-25227000	Weak transcription	HSMM	muscle
11	chr20:25222000-25227200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:25222000-25227400	Weak transcription	Fetal Kidney	kidney
13	chr20:25222000-25227400	Weak transcription	HSMMtube	muscle
14	chr20:25222000-25227600	Weak transcription	Fetal Lung	lung
15	chr20:25222400-25227000	Weak transcription	K562	blood
16	chr20:25222400-25227400	Weak transcription	NH-A	brain
17	chr20:25223200-25227400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr20:25223400-25227400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr20:25223600-25227800	Weak transcription	Brain Germinal Matrix	brain
20	chr20:25223800-25227600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr20:25225800-25227000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr20:25226000-25227000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr20:25226000-25227000	Enhancers	NHEK	skin
24	chr20:25226000-25227200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr20:25226000-25227200	Enhancers	Fetal Heart	heart
26	chr20:25226000-25227400	Enhancers	Hela-S3	cervix
27	chr20:25226200-25227000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr20:25226200-25227000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr20:25226200-25227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr20:25226200-25227200	Weak transcription	Colonic Mucosa	Colon
31	chr20:25226200-25227600	Enhancers	Fetal Intestine Large	intestine
32	chr20:25226200-25227600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr20:25226200-25227600	Enhancers	GM12878-XiMat	blood
34	chr20:25226600-25227400	Weak transcription	HUVEC	blood vessel
35	chr20:25226600-25227600	Enhancers	Fetal Intestine Small	intestine
36	chr20:25226800-25227000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:25226800-25227000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:25226800-25227000	Enhancers	Adipose Nuclei	Adipose
39	chr20:25226800-25227200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr20:25226800-25227200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
41	chr20:25226800-25227200	Enhancers	Duodenum Mucosa	Duodenum
42	chr20:25226800-25227200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr20:25226800-25227200	Enhancers	Stomach Mucosa	stomach
44	chr20:25226800-25227200	Bivalent Enhancer	HepG2	liver
45	chr20:25226800-25227400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr20:25226800-25227400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr20:25226800-25227400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr20:25226800-25227600	Enhancers	Right Ventricle	heart
49	chr20:25226800-25227800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr20:25226800-25227800	Flanking Active TSS	A549	lung

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