Variant report

Variant	rs558014553
Chromosome Location	chr2:20425396-20425397
allele	A/G
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	SP1	chr2:20424249-20425583	A549	lung:	n/a	chr2:20424895-20424909 chr2:20424470-20424482 chr2:20425525-20425534 chr2:20424990-20424999 chr2:20424936-20424946 chr2:20424951-20424961 chr2:20424950-20424962 chr2:20424471-20424485 chr2:20424991-20425000 chr2:20424950-20424962 chr2:20424896-20424905 chr2:20424989-20425001 chr2:20425525-20425535 chr2:20424951-20424960 chr2:20425524-20425536 chr2:20424951-20424960 chr2:20425524-20425536 chr2:20424990-20425000 chr2:20424951-20424965 chr2:20424472-20424481 chr2:20424895-20424905 chr2:20424989-20425001 chr2:20424990-20425000 chr2:20424952-20424961 chr2:20424951-20424961
2	SIN3A	chr2:20422973-20425643	H1-hESC	embryonic stem cell:	n/a	chr2:20425301-20425312 chr2:20424997-20425010 chr2:20424672-20424683 chr2:20424735-20424748 chr2:20424645-20424656
3	RUNX3	chr2:20425013-20425407	GM12878	blood:	n/a	chr2:20425075-20425090
4	MYC	chr2:20425160-20425413	MCF-7	breast:	n/a	n/a
5	MXI1	chr2:20425157-20425482	Hela-S3	cervix:	n/a	n/a
6	MAX	chr2:20424187-20425508	HCT-116	colon:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
7	SMC3	chr2:20425017-20425541	GM12878	blood:	n/a	n/a
8	RAD21	chr2:20420269-20426598	SK-N-SH	brain:	n/a	chr2:20422198-20422210 chr2:20424162-20424172 chr2:20425226-20425238 chr2:20423347-20423361
9	NFIC	chr2:20424972-20426031	HepG2	liver:	n/a	n/a
10	CTCF	chr2:20425065-20425405	GM12892	blood:	n/a	chr2:20425315-20425325
11	EGR1	chr2:20424669-20425725	MCF-7	breast:	n/a	chr2:20424997-20425007 chr2:20424952-20424962 chr2:20424953-20424966 chr2:20425523-20425532 chr2:20424992-20425005 chr2:20425304-20425314 chr2:20425520-20425533
12	RAD21	chr2:20425012-20425440	H1-hESC	embryonic stem cell:	n/a	chr2:20425226-20425238
13	CTCF	chr2:20425038-20425577	IMR90	lung:	n/a	chr2:20425315-20425325
14	MAZ	chr2:20424983-20425428	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr2:20422750-20425544	GM12892	blood:	n/a	n/a
16	CTCF	chr2:20424971-20425427	K562	blood:	n/a	chr2:20425315-20425325
17	POLR2A	chr2:20424965-20425399	H1-neurons	neurons:	n/a	n/a
18	SP1	chr2:20425011-20425430	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:20424370-20425723	MCF-7	breast:	n/a	n/a
20	MXI1	chr2:20425060-20425472	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:20424950-20425955	HepG2	liver:	n/a	n/a
22	MAX	chr2:20423602-20425541	A549	lung:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
23	ESRRA	chr2:20424274-20426108	GM12878	blood:	n/a	chr2:20425299-20425312 chr2:20425885-20425901
24	PAX5	chr2:20424978-20425401	GM12878	blood:	n/a	n/a
25	NFATC1	chr2:20424965-20425409	GM12878	blood:	n/a	n/a
26	CTCF	chr2:20425380-20425530	HPF	lung:	n/a	n/a
27	ZNF263	chr2:20424394-20426249	HEK293-T-REx	kidney:	n/a	n/a
28	HNF4G	chr2:20425019-20425976	HepG2	liver:	n/a	chr2:20425615-20425627 chr2:20425808-20425822 chr2:20425809-20425822
29	RCOR1	chr2:20425053-20425452	HepG2	liver:	n/a	n/a
30	RAD21	chr2:20424977-20425759	MCF-7	breast:	n/a	chr2:20425226-20425238
31	TAF1	chr2:20424959-20425806	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr2:20422503-20426249	HepG2	liver:	n/a	chr2:20423191-20423198 chr2:20424483-20424490 chr2:20423189-20423200 chr2:20424338-20424348 chr2:20423190-20423199 chr2:20423540-20423550 chr2:20423190-20423200 chr2:20424526-20424536 chr2:20423189-20423199
33	PAX5	chr2:20424923-20425501	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:20423054-20425551	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr2:20422936-20425902	MCF-7	breast:	n/a	n/a
36	RAD21	chr2:20424784-20425815	HCT-116	colon:	n/a	chr2:20425226-20425238
37	ZNF143	chr2:20425130-20425846	H1-hESC	embryonic stem cell:	n/a	n/a
38	NR2F2	chr2:20424957-20426048	MCF-7	breast:	n/a	n/a
39	EP300	chr2:20424967-20425538	A549	lung:	n/a	chr2:20425152-20425168 chr2:20425173-20425189
40	MAZ	chr2:20424731-20425542	GM12878	blood:	n/a	n/a
41	GTF2F1	chr2:20425270-20425831	H1-hESC	embryonic stem cell:	n/a	n/a
42	HDAC2	chr2:20422965-20425963	HepG2	liver:	n/a	n/a
43	RAD21	chr2:20425086-20425413	Hela-S3	cervix:	n/a	chr2:20425226-20425238
44	MYBL2	chr2:20424962-20425949	HepG2	liver:	n/a	n/a
45	CTCF	chr2:20425018-20425414	A549	lung:	n/a	chr2:20425315-20425325
46	RFX5	chr2:20425108-20425459	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr2:20425078-20425404	GM19238	blood:	n/a	chr2:20425315-20425325
48	PAX5	chr2:20424945-20425500	GM12892	blood:	n/a	n/a
49	MAX	chr2:20424253-20425899	MCF-7	breast:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
50	RAD21	chr2:20425036-20425421	IMR90	lung:	n/a	chr2:20425226-20425238

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:20425395-20425445	HRPEpiC	eye:	n/a
2	chr2:20425395-20425445	HCM	heart:	n/a
3	chr2:20425395-20425445	ECC-1	luminal epithelium:	n/a
4	chr2:20425395-20425445	NT2-D1	testis:	n/a
5	chr2:20425395-20425445	PrEC	prostate:	n/a
6	chr2:20425395-20425445	SAEC	small airway:	n/a
7	chr2:20425395-20425445	A549	lung:	n/a
8	chr2:20425395-20425445	ovcar-3	ovarian:	n/a
9	chr2:20425395-20425445	HNPCEpiC	eye:	n/a
10	chr2:20425395-20425445	HIPEpiC	eye:	n/a
11	chr2:20425395-20425445	LNCaP	prostate:	n/a
12	chr2:20425395-20425445	AoSMC	blood vessel:	n/a
13	chr2:20425395-20425445	GM12878	blood:	n/a
14	chr2:20425395-20425445	AG10803	skin:	n/a
15	chr2:20425395-20425445	Caco-2	colon:	n/a
16	chr2:20425395-20425445	HCF	heart:	n/a
17	chr2:20425395-20425445	H1-hESC	embryonic stem cell:	embryo
18	chr2:20425395-20425445	HAEpiC	amniotic membrane:	n/a
19	chr2:20425395-20425445	IMR90	lung:	fetal
20	chr2:20425395-20425445	SK-N-SH_RA	brain:	n/a
21	chr2:20425395-20425445	PFSK-1	brain:	n/a
22	chr2:20425395-20425445	NHDF-neo	bronchial:	n/a
23	chr2:20425395-20425445	MCF-7	breast:	n/a
24	chr2:20425395-20425445	HEEpiC	esophagus:	n/a
25	chr2:20425395-20425445	U87	brain:	n/a
26	chr2:20425395-20425445	MCF10A-Er-Src	breast:	n/a
27	chr2:20425395-20425445	NB4	blood:	n/a
28	chr2:20425395-20425445	NHBE	bronchial:	n/a
29	chr2:20425395-20425445	Hela-S3	cervix:	n/a
30	chr2:20425395-20425445	K562	blood:	n/a
31	chr2:20425395-20425445	HMEC	breast:	n/a
32	chr2:20425395-20425445	HRCEpiC	kidney:	n/a
33	chr2:20425395-20425445	CMK	blood:	n/a
34	chr2:20425395-20425445	HL-60	blood:	n/a
35	chr2:20425395-20425445	HCT-116	colon:	n/a
36	chr2:20425395-20425445	HEK293	kidney:	embryo
37	chr2:20425395-20425445	HUVEC	blood vessel:	n/a
38	chr2:20425395-20425445	Jurkat	blood:	n/a
39	chr2:20425395-20425445	AG04450	lung:	fetal
40	chr2:20425395-20425445	ProgFib	skin:	n/a
41	chr2:20425395-20425445	T-47D	breast:	n/a
42	chr2:20425395-20425445	PANC-1	pancreas:	n/a
43	chr2:20425395-20425445	SK-N-MC	brain:	n/a
44	chr2:20425395-20425445	Hepatocyte	liver:	n/a
45	chr2:20425395-20425445	GM12892	blood:	n/a
46	chr2:20425395-20425445	BE2_C	brain:	n/a
47	chr2:20425395-20425445	AG09309	skin:	n/a
48	chr2:20425395-20425445	HRE	kidney:	n/a
49	chr2:20425395-20425445	NH-A	brain:	n/a
50	chr2:20425395-20425445	GM06990	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20299695..20307724-chr2:20421846..20426859,15	MCF-7	breast:
2	chr2:20306351..20307044-chr2:20424834..20425592,2	MCF-7	breast:
3	chr2:20424066..20426931-chr2:20646792..20649592,2	MCF-7	breast:
4	chr2:20422608..20425941-chr2:20442995..20447318,5	MCF-7	breast:
5	chr2:20249233..20252415-chr2:20424056..20425890,4	MCF-7	breast:
6	chr2:20097107..20100415-chr2:20424161..20425989,3	K562	blood:
7	chr2:20421499..20423791-chr2:20425335..20427623,2	K562	blood:

Variant related genes	Relation type
SDC1	TF binding region
SDC1	CpG island
ENSG00000234378	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000238735	Chromatin interaction
ENSG00000115884	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000223734	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846803	chr2:20409322-20427189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	esv3429530	chr2:20423096-20425644	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	esv1798036	chr2:20423264-20442631	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1846193	chr2:20423264-20442631	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv1849406	chr2:20423264-20442631	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1819683	chr2:20423264-20455467	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3398925	chr2:20423871-20426119	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 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	chr2:20422600-20425600	Active TSS	Fetal Brain Female	brain
2	chr2:20422600-20425800	Active TSS	Rectal Smooth Muscle	rectum
3	chr2:20422800-20425400	Active TSS	Brain Angular Gyrus	brain
4	chr2:20422800-20425400	Active TSS	A549	lung
5	chr2:20422800-20425400	Active TSS	HMEC	breast
6	chr2:20422800-20425600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:20422800-20425600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:20422800-20425600	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr2:20422800-20426000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:20423000-20425400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:20423000-20425400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:20423000-20425400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:20423000-20425400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr2:20423000-20425400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr2:20423000-20425400	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr2:20423000-20425400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:20423000-20425400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
18	chr2:20423000-20425400	Weak transcription	Fetal Heart	heart
19	chr2:20423000-20425400	Active TSS	Fetal Intestine Small	intestine
20	chr2:20423000-20425400	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr2:20423000-20425400	Active TSS	Fetal Lung	lung
22	chr2:20423000-20425400	Active TSS	Ovary	ovary
23	chr2:20423000-20425400	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr2:20423000-20425400	Active TSS	NHDF-Ad	bronchial
25	chr2:20423000-20425600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:20423000-20425600	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr2:20423000-20425600	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr2:20423000-20425600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:20423000-20425600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:20423000-20425600	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:20423000-20425600	Active TSS	Colon Smooth Muscle	Colon
32	chr2:20423000-20425600	Active TSS	Hela-S3	cervix
33	chr2:20423000-20425800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr2:20423000-20425800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:20423000-20425800	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr2:20423000-20425800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:20423200-20425400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:20423200-20425400	Active TSS	Aorta	Aorta
39	chr2:20423200-20425400	Active TSS	Duodenum Mucosa	Duodenum
40	chr2:20423200-20425400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
41	chr2:20423200-20425400	Active TSS	Fetal Intestine Large	intestine
42	chr2:20423200-20425400	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr2:20423200-20425400	Active TSS	HepG2	liver
44	chr2:20423200-20425400	Active TSS	HSMM	muscle
45	chr2:20423200-20425400	Active TSS	NH-A	brain
46	chr2:20423200-20425400	Active TSS	Osteobl	bone
47	chr2:20423200-20425600	Active TSS	H1 Cell Line	embryonic stem cell
48	chr2:20423200-20425600	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr2:20423200-20425600	Active TSS	HSMMtube	muscle
50	chr2:20423400-20425400	Active TSS	Pancreas	Pancrea

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