Variant report

Variant	rs3746331
Chromosome Location	chr20:25039046-25039047
allele	A/C
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	ZNF143	chr20:25037916-25039172	GM12878	blood:	n/a	chr20:25038901-25038919 chr20:25038046-25038064
2	POLR2A	chr20:25038586-25039621	GM12878	blood:	n/a	n/a
3	JUND	chr20:25038728-25039180	A549	lung:	n/a	chr20:25038915-25038924
4	PAX5	chr20:25038755-25039268	GM12878	blood:	n/a	chr20:25039002-25039021
5	PAX5	chr20:25038855-25039150	GM12878	blood:	n/a	chr20:25039002-25039021
6	MAX	chr20:25037443-25039443	HepG2	liver:	n/a	chr20:25038195-25038205 chr20:25038194-25038204 chr20:25038197-25038204 chr20:25038195-25038206
7	ATF2	chr20:25038885-25039238	GM12878	blood:	n/a	n/a
8	YY1	chr20:25038508-25039166	GM12891	blood:	n/a	chr20:25038728-25038748
9	CHD2	chr20:25038952-25039199	H1-hESC	embryonic stem cell:	n/a	chr20:25039157-25039167
10	TAF1	chr20:25038925-25039202	GM12878	blood:	n/a	n/a
11	POLR2A	chr20:25037821-25039200	A549	lung:	n/a	n/a
12	PML	chr20:25038604-25039609	GM12878	blood:	n/a	n/a
13	MAX	chr20:25037743-25039467	GM12878	blood:	n/a	chr20:25038195-25038205 chr20:25038194-25038204 chr20:25038197-25038204 chr20:25038195-25038206
14	PAX5	chr20:25038502-25039414	GM12878	blood:	n/a	chr20:25039002-25039021
15	MYC	chr20:25037636-25039202	A549	lung:	n/a	chr20:25038195-25038205 chr20:25038194-25038204 chr20:25038197-25038204 chr20:25038195-25038206
16	TCF3	chr20:25038418-25039290	GM12878	blood:	n/a	n/a
17	ELK1	chr20:25038678-25039252	GM12878	blood:	n/a	n/a
18	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
19	POLR2A	chr20:25038860-25039149	GM12891	blood:	n/a	n/a
20	CHD2	chr20:25038804-25039546	GM12878	blood:	n/a	chr20:25039369-25039376 chr20:25039157-25039167
21	RELA	chr20:25037759-25039318	GM12891	blood:	n/a	chr20:25038013-25038022 chr20:25038013-25038022
22	POLR2A	chr20:25037547-25039348	HL-60	blood:	n/a	n/a
23	POLR2A	chr20:25037745-25039148	HepG2	liver:	n/a	n/a
24	MAX	chr20:25038954-25039216	K562	blood:	n/a	n/a
25	MAX	chr20:25038935-25039272	A549	lung:	n/a	n/a
26	ELF1	chr20:25037470-25039777	GM12878	blood:	n/a	chr20:25038810-25038822 chr20:25037890-25037902 chr20:25038816-25038828 chr20:25037943-25037955
27	PAX5	chr20:25038471-25039518	GM12892	blood:	n/a	chr20:25039002-25039021
28	EP300	chr20:25038940-25039531	GM12878	blood:	n/a	n/a
29	IRF4	chr20:25038940-25039251	GM12878	blood:	n/a	chr20:25039053-25039067 chr20:25039057-25039071
30	EP300	chr20:25038985-25039130	GM12878	blood:	n/a	n/a
31	TCF12	chr20:25038938-25039225	GM12878	blood:	n/a	n/a
32	POLR2A	chr20:25037622-25039895	GM12878	blood:	n/a	n/a
33	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
34	POLR2A	chr20:25038453-25039418	GM12891	blood:	n/a	n/a
35	POLR2A	chr20:25037831-25039540	GM12878	blood:	n/a	n/a
36	YY1	chr20:25038429-25039220	GM12892	blood:	n/a	chr20:25038728-25038748
37	POLR2A	chr20:25037476-25039581	GM12892	blood:	n/a	n/a
38	YY1	chr20:25038585-25039227	GM12878	blood:	n/a	chr20:25038728-25038748
39	CTBP2	chr20:25037729-25039406	H1-hESC	embryonic stem cell:	n/a	n/a
40	BHLHE40	chr20:25038937-25039306	HepG2	liver:	n/a	chr20:25039115-25039124 chr20:25039115-25039124 chr20:25039114-25039123 chr20:25039109-25039130
41	POLR2A	chr20:25037997-25039251	HUVEC	blood vessel:	n/a	n/a
42	STAT1	chr20:25037865-25039312	GM12878	blood:	n/a	chr20:25038908-25038920
43	MAZ	chr20:25037777-25039616	GM12878	blood:	n/a	chr20:25038195-25038205 chr20:25038197-25038204 chr20:25038195-25038206
44	POLR2A	chr20:25037393-25039568	GM12878	blood:	n/a	n/a
45	PAX5	chr20:25038776-25039096	GM12891	blood:	n/a	chr20:25039002-25039021
46	MAX	chr20:25038904-25039352	SK-N-SH	brain:	n/a	n/a
47	MAX	chr20:25038948-25039280	HepG2	liver:	n/a	n/a
48	MAX	chr20:25038718-25039420	SK-N-SH	brain:	n/a	n/a
49	TCF12	chr20:25038558-25039142	ECC-1	luminal epithelium:	n/a	n/a
50	TBL1XR1	chr20:25037738-25039674	GM12878	blood:	n/a	n/a

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: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2207632	0.82[EUR][1000 genomes]
rs3646	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815365	0.84[EUR][1000 genomes]
rs55651034	0.81[EUR][1000 genomes]
rs62217194	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62217195	0.80[EUR][1000 genomes]
rs62217196	0.81[EUR][1000 genomes]
rs7265721	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7265950	0.81[EUR][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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25036800-25039200	Active TSS	Fetal Intestine Large	intestine
2	chr20:25037200-25039800	Active TSS	Aorta	Aorta
3	chr20:25037400-25039200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr20:25037400-25039200	Active TSS	Brain Angular Gyrus	brain
5	chr20:25037400-25039200	Active TSS	Fetal Intestine Small	intestine
6	chr20:25037400-25039400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr20:25037400-25039600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:25037400-25039600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr20:25037400-25039600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr20:25037400-25039600	Active TSS	Ovary	ovary
11	chr20:25037400-25040200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr20:25037600-25039200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr20:25037600-25039200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr20:25037600-25039200	Active TSS	Brain Anterior Caudate	brain
15	chr20:25037600-25039200	Active TSS	Fetal Lung	lung
16	chr20:25037600-25039200	Active TSS	Pancreas	Pancrea
17	chr20:25037600-25039200	Active TSS	Placenta Amnion	Placenta Amnion
18	chr20:25037600-25039200	Active TSS	Right Atrium	heart
19	chr20:25037600-25039200	Active TSS	A549	lung
20	chr20:25037600-25039400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr20:25037600-25039400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr20:25037600-25039400	Active TSS	Gastric	stomach
23	chr20:25037600-25039600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
24	chr20:25037600-25039600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr20:25037600-25039600	Active TSS	Colon Smooth Muscle	Colon
26	chr20:25037600-25039600	Active TSS	Left Ventricle	heart
27	chr20:25037600-25039600	Active TSS	Small Intestine	intestine
28	chr20:25037600-25039800	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr20:25037600-25039800	Active TSS	Fetal Kidney	kidney
30	chr20:25037600-25039800	Active TSS	Rectal Smooth Muscle	rectum
31	chr20:25037600-25039800	Active TSS	Right Ventricle	heart
32	chr20:25037800-25039200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr20:25037800-25039200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr20:25037800-25039200	Active TSS	Primary monocytes fromperipheralblood	blood
35	chr20:25037800-25039200	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr20:25037800-25039200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr20:25037800-25039200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr20:25037800-25039200	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr20:25037800-25039200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr20:25037800-25039200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr20:25037800-25039200	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr20:25037800-25039200	Active TSS	Brain Substantia Nigra	brain
43	chr20:25037800-25039200	Active TSS	Esophagus	oesophagus
44	chr20:25037800-25039200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr20:25037800-25039200	Active TSS	Fetal Stomach	stomach
46	chr20:25037800-25039200	Active TSS	Lung	lung
47	chr20:25037800-25039200	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr20:25037800-25039400	Bivalent/Poised TSS	HSMM	muscle
49	chr20:25037800-25039400	Bivalent/Poised TSS	HSMMtube	muscle
50	chr20:25037800-25039400	Active TSS	NHDF-Ad	bronchial

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