Variant report

Variant	rs73906075
Chromosome Location	chr20:25039267-25039268
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	chr20:25038586-25039621	GM12878	blood:	n/a	n/a
2	PAX5	chr20:25038755-25039268	GM12878	blood:	n/a	chr20:25039002-25039021
3	MAX	chr20:25037443-25039443	HepG2	liver:	n/a	chr20:25038195-25038205 chr20:25038194-25038204 chr20:25038197-25038204 chr20:25038195-25038206
4	PML	chr20:25038604-25039609	GM12878	blood:	n/a	n/a
5	MAX	chr20:25037743-25039467	GM12878	blood:	n/a	chr20:25038195-25038205 chr20:25038194-25038204 chr20:25038197-25038204 chr20:25038195-25038206
6	PAX5	chr20:25038502-25039414	GM12878	blood:	n/a	chr20:25039002-25039021
7	TCF3	chr20:25038418-25039290	GM12878	blood:	n/a	n/a
8	SP1	chr20:25038627-25039291	GM12878	blood:	n/a	chr20:25038816-25038825 chr20:25038969-25038978 chr20:25038816-25038826 chr20:25038816-25038826 chr20:25038815-25038827 chr20:25038816-25038825 chr20:25038815-25038827 chr20:25038817-25038826
9	CHD2	chr20:25038804-25039546	GM12878	blood:	n/a	chr20:25039369-25039376 chr20:25039157-25039167
10	RELA	chr20:25037759-25039318	GM12891	blood:	n/a	chr20:25038013-25038022 chr20:25038013-25038022
11	POLR2A	chr20:25037547-25039348	HL-60	blood:	n/a	n/a
12	MAX	chr20:25038935-25039272	A549	lung:	n/a	n/a
13	ELF1	chr20:25037470-25039777	GM12878	blood:	n/a	chr20:25038810-25038822 chr20:25037890-25037902 chr20:25038816-25038828 chr20:25037943-25037955
14	PAX5	chr20:25038471-25039518	GM12892	blood:	n/a	chr20:25039002-25039021
15	EP300	chr20:25038940-25039531	GM12878	blood:	n/a	n/a
16	POLR2A	chr20:25037622-25039895	GM12878	blood:	n/a	n/a
17	BHLHE40	chr20:25037730-25040053	GM12878	blood:	n/a	chr20:25038140-25038156 chr20:25039115-25039124 chr20:25038316-25038332 chr20:25039115-25039124 chr20:25039114-25039123 chr20:25039109-25039130
18	POLR2A	chr20:25038453-25039418	GM12891	blood:	n/a	n/a
19	POLR2A	chr20:25037831-25039540	GM12878	blood:	n/a	n/a
20	POLR2A	chr20:25037476-25039581	GM12892	blood:	n/a	n/a
21	CTBP2	chr20:25037729-25039406	H1-hESC	embryonic stem cell:	n/a	n/a
22	BHLHE40	chr20:25038937-25039306	HepG2	liver:	n/a	chr20:25039115-25039124 chr20:25039115-25039124 chr20:25039114-25039123 chr20:25039109-25039130
23	STAT1	chr20:25037865-25039312	GM12878	blood:	n/a	chr20:25038908-25038920
24	MAZ	chr20:25037777-25039616	GM12878	blood:	n/a	chr20:25038195-25038205 chr20:25038197-25038204 chr20:25038195-25038206
25	POLR2A	chr20:25037393-25039568	GM12878	blood:	n/a	n/a
26	MAX	chr20:25038904-25039352	SK-N-SH	brain:	n/a	n/a
27	MAX	chr20:25038948-25039280	HepG2	liver:	n/a	n/a
28	MAX	chr20:25038718-25039420	SK-N-SH	brain:	n/a	n/a
29	TBL1XR1	chr20:25037738-25039674	GM12878	blood:	n/a	n/a
30	BCLAF1	chr20:25038800-25039386	GM12878	blood:	n/a	chr20:25038820-25038833 chr20:25038969-25038978
31	MAX	chr20:25037440-25039514	A549	lung:	n/a	chr20:25038195-25038205 chr20:25038194-25038204 chr20:25038197-25038204 chr20:25038195-25038206
32	STAT5A	chr20:25038737-25039403	GM12878	blood:	n/a	chr20:25038908-25038920
33	ZBTB7A	chr20:25038065-25039430	ECC-1	luminal epithelium:	n/a	chr20:25038858-25038866
34	BCLAF1	chr20:25038888-25039316	GM12878	blood:	n/a	chr20:25038969-25038978
35	POU2F2	chr20:25038525-25039314	GM12878	blood:	n/a	chr20:25038819-25038831 chr20:25038816-25038828
36	SIN3A	chr20:25038911-25039279	GM12878	blood:	n/a	chr20:25038997-25039006 chr20:25038988-25039001
37	CTCF	chr20:25039180-25039330	AG04449	skin:	n/a	n/a
38	CHD1	chr20:25037336-25039386	GM12878	blood:	n/a	chr20:25039369-25039376 chr20:25039157-25039167
39	TAF1	chr20:25038552-25039323	GM12878	blood:	n/a	n/a
40	POLR2A	chr20:25036593-25039599	PBDE	blood:	n/a	n/a
41	POLR2A	chr20:25037542-25039518	GM19193	blood:	n/a	n/a
42	POLR2A	chr20:25037666-25039438	GM18526	blood:	n/a	n/a
43	SPI1	chr20:25039117-25039370	GM12878	blood:	n/a	n/a
44	POLR2A	chr20:25037748-25039562	GM12891	blood:	n/a	n/a
45	POLR2A	chr20:25037651-25040149	GM12878	blood:	n/a	n/a
46	POLR2A	chr20:25037441-25039609	GM18505	blood:	n/a	n/a
47	POU2F2	chr20:25038805-25039321	GM12891	blood:	n/a	chr20:25038819-25038831 chr20:25038816-25038828
48	POLR2A	chr20:25038801-25039336	GM12892	blood:	n/a	n/a
49	MAX	chr20:25038817-25039334	ECC-1	luminal epithelium:	n/a	n/a
50	RELA	chr20:25037773-25039344	GM10847	blood:	n/a	chr20:25038013-25038022 chr20:25038013-25038022

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24970831..24976063-chr20:25037253..25040567,5	MCF-7	breast:

Variant related genes	Relation type
ACSS1	TF binding region
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11907003	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35022349	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7268196	1.00[AMR][1000 genomes]
rs7270954	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9967918	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	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
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25037200-25039800	Active TSS	Aorta	Aorta
2	chr20:25037400-25039400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
3	chr20:25037400-25039600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:25037400-25039600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:25037400-25039600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr20:25037400-25039600	Active TSS	Ovary	ovary
7	chr20:25037400-25040200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr20:25037600-25039400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr20:25037600-25039400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr20:25037600-25039400	Active TSS	Gastric	stomach
11	chr20:25037600-25039600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr20:25037600-25039600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr20:25037600-25039600	Active TSS	Colon Smooth Muscle	Colon
14	chr20:25037600-25039600	Active TSS	Left Ventricle	heart
15	chr20:25037600-25039600	Active TSS	Small Intestine	intestine
16	chr20:25037600-25039800	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr20:25037600-25039800	Active TSS	Fetal Kidney	kidney
18	chr20:25037600-25039800	Active TSS	Rectal Smooth Muscle	rectum
19	chr20:25037600-25039800	Active TSS	Right Ventricle	heart
20	chr20:25037800-25039400	Bivalent/Poised TSS	HSMM	muscle
21	chr20:25037800-25039400	Bivalent/Poised TSS	HSMMtube	muscle
22	chr20:25037800-25039400	Active TSS	NHDF-Ad	bronchial
23	chr20:25037800-25039600	Active TSS	Colonic Mucosa	Colon
24	chr20:25037800-25039600	Active TSS	Psoas Muscle	Psoas
25	chr20:25037800-25039600	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr20:25037800-25039600	Active TSS	Thymus	Thymus
27	chr20:25037800-25040000	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr20:25037800-25040000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr20:25038000-25039600	Bivalent/Poised TSS	NHEK	skin
30	chr20:25038000-25039800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr20:25038200-25039400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
32	chr20:25038200-25039400	Flanking Active TSS	Liver	Liver
33	chr20:25038200-25040000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr20:25038600-25039400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
35	chr20:25038600-25039400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr20:25038600-25039600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr20:25038600-25039600	Bivalent Enhancer	Fetal Brain Male	brain
38	chr20:25038600-25039800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:25038800-25039400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr20:25038800-25039600	Flanking Bivalent TSS/Enh	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr20:25039000-25039400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
42	chr20:25039000-25039400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr20:25039000-25039400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr20:25039000-25039400	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr20:25039000-25039400	Flanking Bivalent TSS/Enh	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr20:25039000-25039400	Flanking Active TSS	HMEC	breast
47	chr20:25039000-25039400	Flanking Bivalent TSS/Enh	NHLF	lung
48	chr20:25039000-25039600	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr20:25039000-25039600	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr20:25039000-25039600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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