Variant report

Variant	rs535280458
Chromosome Location	chr2:20425194-20425195
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	CTCF	chr2:20425180-20425330	HRPEpiC	eye:	n/a	chr2:20425315-20425325
4	MAX	chr2:20425076-20425394	NB4	blood:	n/a	n/a
5	RUNX3	chr2:20425013-20425407	GM12878	blood:	n/a	chr2:20425075-20425090
6	CTCF	chr2:20425140-20425290	SK-N-SH_RA	brain:	n/a	n/a
7	MYC	chr2:20425160-20425413	MCF-7	breast:	n/a	n/a
8	POLR2A	chr2:20424955-20425371	H1-neurons	neurons:	n/a	n/a
9	CTCF	chr2:20425160-20425310	AG04449	skin:	n/a	n/a
10	MAX	chr2:20425130-20425324	K562	blood:	n/a	n/a
11	ZNF143	chr2:20425075-20425295	Hela-S3	cervix:	n/a	chr2:20425113-20425131
12	MXI1	chr2:20425157-20425482	Hela-S3	cervix:	n/a	n/a
13	MAX	chr2:20424187-20425508	HCT-116	colon:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
14	SMC3	chr2:20425017-20425541	GM12878	blood:	n/a	n/a
15	BRCA1	chr2:20425175-20425272	HepG2	liver:	n/a	n/a
16	RAD21	chr2:20420269-20426598	SK-N-SH	brain:	n/a	chr2:20422198-20422210 chr2:20424162-20424172 chr2:20425226-20425238 chr2:20423347-20423361
17	NFIC	chr2:20424972-20426031	HepG2	liver:	n/a	n/a
18	CTCF	chr2:20425065-20425405	GM12892	blood:	n/a	chr2:20425315-20425325
19	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
20	CTCF	chr2:20425074-20425359	A549	lung:	n/a	chr2:20425315-20425325
21	RAD21	chr2:20425012-20425440	H1-hESC	embryonic stem cell:	n/a	chr2:20425226-20425238
22	MXI1	chr2:20425064-20425255	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr2:20425038-20425577	IMR90	lung:	n/a	chr2:20425315-20425325
24	CTCF	chr2:20425087-20425383	NHEK	skin:	n/a	chr2:20425315-20425325
25	MAZ	chr2:20424983-20425428	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr2:20424936-20425362	SK-N-SH_RA	brain:	n/a	chr2:20425226-20425238
27	CTCF	chr2:20425180-20425330	BJ	skin:	n/a	chr2:20425315-20425325
28	POLR2A	chr2:20422750-20425544	GM12892	blood:	n/a	n/a
29	CTCF	chr2:20424971-20425427	K562	blood:	n/a	chr2:20425315-20425325
30	CTCF	chr2:20425083-20425355	K562	blood:	n/a	chr2:20425315-20425325
31	POLR2A	chr2:20424965-20425399	H1-neurons	neurons:	n/a	n/a
32	SP1	chr2:20425011-20425430	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:20424370-20425723	MCF-7	breast:	n/a	n/a
34	CTCF	chr2:20425098-20425305	Spleen_OC	spleen:	n/a	n/a
35	NFIC	chr2:20424220-20425356	ECC-1	luminal epithelium:	n/a	n/a
36	MXI1	chr2:20425060-20425472	GM12878	blood:	n/a	n/a
37	CTCF	chr2:20425160-20425310	GM12866	blood:	n/a	n/a
38	POLR2A	chr2:20424950-20425955	HepG2	liver:	n/a	n/a
39	MAX	chr2:20423602-20425541	A549	lung:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
40	CTCF	chr2:20425180-20425330	HMEC	breast:	n/a	chr2:20425315-20425325
41	CTCF	chr2:20425160-20425310	HCT-116	colon:	n/a	n/a
42	ESRRA	chr2:20424274-20426108	GM12878	blood:	n/a	chr2:20425299-20425312 chr2:20425885-20425901
43	CTCF	chr2:20425160-20425310	GM12869	blood:	n/a	n/a
44	PAX5	chr2:20424978-20425401	GM12878	blood:	n/a	n/a
45	NFATC1	chr2:20424965-20425409	GM12878	blood:	n/a	n/a
46	CTCF	chr2:20425160-20425310	GM12864	blood:	n/a	n/a
47	CTCF	chr2:20425160-20425310	GM06990	blood:	n/a	n/a
48	ZNF263	chr2:20424394-20426249	HEK293-T-REx	kidney:	n/a	n/a
49	CTCF	chr2:20425120-20425270	GM12878	blood:	n/a	n/a
50	HNF4G	chr2:20425019-20425976	HepG2	liver:	n/a	chr2:20425615-20425627 chr2:20425808-20425822 chr2:20425809-20425822

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	chr2:20423460..20425374-chr2:20445845..20448782,3	MCF-7	breast:

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

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv15661	chr2:20423227-20425210	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20422000-20425200	Active TSS	Esophagus	oesophagus
2	chr2:20422200-20425200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:20422600-20425600	Active TSS	Fetal Brain Female	brain
4	chr2:20422600-20425800	Active TSS	Rectal Smooth Muscle	rectum
5	chr2:20422800-20425400	Active TSS	Brain Angular Gyrus	brain
6	chr2:20422800-20425400	Active TSS	A549	lung
7	chr2:20422800-20425400	Active TSS	HMEC	breast
8	chr2:20422800-20425600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:20422800-20425600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:20422800-20425600	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr2:20422800-20426000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:20423000-20425200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:20423000-20425200	Active TSS	Placenta Amnion	Placenta Amnion
14	chr2:20423000-20425200	Active TSS	Right Ventricle	heart
15	chr2:20423000-20425400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr2:20423000-20425400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:20423000-20425400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:20423000-20425400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr2:20423000-20425400	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr2:20423000-20425400	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr2:20423000-20425400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:20423000-20425400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
23	chr2:20423000-20425400	Weak transcription	Fetal Heart	heart
24	chr2:20423000-20425400	Active TSS	Fetal Intestine Small	intestine
25	chr2:20423000-20425400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr2:20423000-20425400	Active TSS	Fetal Lung	lung
27	chr2:20423000-20425400	Active TSS	Ovary	ovary
28	chr2:20423000-20425400	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr2:20423000-20425400	Active TSS	NHDF-Ad	bronchial
30	chr2:20423000-20425600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:20423000-20425600	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr2:20423000-20425600	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr2:20423000-20425600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:20423000-20425600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:20423000-20425600	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr2:20423000-20425600	Active TSS	Colon Smooth Muscle	Colon
37	chr2:20423000-20425600	Active TSS	Hela-S3	cervix
38	chr2:20423000-20425800	Active TSS	H9 Cell Line	embryonic stem cell
39	chr2:20423000-20425800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:20423000-20425800	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr2:20423000-20425800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:20423200-20425200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:20423200-20425200	Active TSS	Brain Substantia Nigra	brain
44	chr2:20423200-20425200	Active TSS	Gastric	stomach
45	chr2:20423200-20425400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:20423200-20425400	Active TSS	Aorta	Aorta
47	chr2:20423200-20425400	Active TSS	Duodenum Mucosa	Duodenum
48	chr2:20423200-20425400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
49	chr2:20423200-20425400	Active TSS	Fetal Intestine Large	intestine
50	chr2:20423200-20425400	Active TSS	Sigmoid Colon	Sigmoid Colon

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