Variant report

Variant	rs536737520
Chromosome Location	chr2:54682500-54682501
allele	A/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	MYBL2	chr2:54681501-54683343	HepG2	liver:	n/a	n/a
2	USF2	chr2:54682404-54682536	HepG2	liver:	n/a	n/a
3	USF1	chr2:54682244-54682545	SK-N-SH_RA	brain:	n/a	chr2:54682429-54682440
4	TEAD4	chr2:54682238-54682586	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr2:54682189-54685375	H1-neurons	neurons:	n/a	n/a
6	MYBL2	chr2:54681631-54683715	HepG2	liver:	n/a	n/a
7	HEY1	chr2:54681566-54683738	HepG2	liver:	n/a	chr2:54683583-54683598 chr2:54683492-54683507
8	YY1	chr2:54682078-54682582	HepG2	liver:	n/a	chr2:54682359-54682371
9	POLR2A	chr2:54682165-54683785	H1-hESC	embryonic stem cell:	n/a	n/a
10	USF2	chr2:54682278-54682613	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:54682183-54682651	HepG2	liver:	n/a	n/a
12	YY1	chr2:54682186-54682552	SK-N-SH_RA	brain:	n/a	chr2:54682359-54682371
13	POLR2A	chr2:54682488-54682817	MCF-7	breast:	n/a	n/a
14	POLR2A	chr2:54681650-54683349	HepG2	liver:	n/a	n/a
15	TAF1	chr2:54682217-54682844	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTBP2	chr2:54682379-54685140	H1-hESC	embryonic stem cell:	n/a	n/a
17	MBD4	chr2:54682085-54683332	HepG2	liver:	n/a	n/a
18	RAD21	chr2:54682269-54682580	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:54682190-54682676	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:54682360-54682660	Gliobla	brain:	n/a	n/a
21	POLR2A	chr2:54682496-54682532	ProgFib	skin:	n/a	n/a
22	MAX	chr2:54682291-54682607	H1-hESC	embryonic stem cell:	n/a	chr2:54682429-54682440
23	MYC	chr2:54682309-54682521	H1-hESC	embryonic stem cell:	n/a	chr2:54682429-54682440
24	FOXA2	chr2:54681127-54682857	HepG2	liver:	n/a	chr2:54681975-54681987
25	USF1	chr2:54682233-54682578	SK-N-SH_RA	brain:	n/a	chr2:54682429-54682440
26	RCOR1	chr2:54682345-54682535	HepG2	liver:	n/a	n/a
27	USF1	chr2:54682272-54682631	H1-hESC	embryonic stem cell:	n/a	chr2:54682429-54682440
28	USF1	chr2:54682242-54682599	H1-hESC	embryonic stem cell:	n/a	chr2:54682429-54682440
29	TBP	chr2:54682320-54682520	H1-hESC	embryonic stem cell:	n/a	n/a
30	NFIC	chr2:54681500-54682550	HepG2	liver:	n/a	n/a
31	MXI1	chr2:54681837-54685789	SK-N-SH	brain:	n/a	n/a
32	YY1	chr2:54682184-54682549	H1-hESC	embryonic stem cell:	n/a	chr2:54682359-54682371
33	CHD2	chr2:54682407-54682567	HepG2	liver:	n/a	n/a
34	USF1	chr2:54682271-54682555	HepG2	liver:	n/a	chr2:54682429-54682440
35	MAX	chr2:54682334-54682568	HepG2	liver:	n/a	chr2:54682429-54682440
36	MBD4	chr2:54681524-54682655	HepG2	liver:	n/a	n/a
37	MAZ	chr2:54682047-54685233	IMR90	lung:	n/a	chr2:54682934-54682942 chr2:54683800-54683809 chr2:54682429-54682440
38	RAD21	chr2:54682223-54682577	H1-hESC	embryonic stem cell:	n/a	n/a
39	TAF1	chr2:54682113-54683746	H1-neurons	neurons:	n/a	n/a
40	TBP	chr2:54682305-54682519	HepG2	liver:	n/a	n/a
41	YY1	chr2:54682200-54682817	HepG2	liver:	n/a	chr2:54682584-54682595 chr2:54682359-54682371
42	POLR2A	chr2:54682284-54683990	HepG2	liver:	n/a	n/a
43	HEY1	chr2:54681893-54683353	HepG2	liver:	n/a	n/a
44	YY1	chr2:54682129-54683355	H1-hESC	embryonic stem cell:	n/a	chr2:54683188-54683199 chr2:54682584-54682595 chr2:54682359-54682371
45	POLR2A	chr2:54682440-54682556	HUVEC	blood vessel:	n/a	n/a
46	REST	chr2:54681921-54685572	H1-neurons	neurons:	n/a	chr2:54683922-54683942 chr2:54684871-54684881 chr2:54683744-54683757
47	POLR2A	chr2:54682123-54685349	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr2:54682467-54682539	A549	lung:	n/a	n/a
49	SIN3A	chr2:54682235-54685210	H1-hESC	embryonic stem cell:	n/a	chr2:54683507-54683520 chr2:54684872-54684881 chr2:54683744-54683757 chr2:54684209-54684220 chr2:54685001-54685012 chr2:54683188-54683199 chr2:54683592-54683603
50	NFIC	chr2:54682232-54683121	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54341520..54343821-chr2:54682367..54684141,3	MCF-7	breast:
2	chr2:54663282..54665058-chr2:54681463..54683178,2	MCF-7	breast:

Variant related genes	Relation type
SPTBN1	TF binding region
ENSG00000170634	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	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3403234	chr2:54681448-54686246	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3407657	chr2:54682273-54685021	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3392501	chr2:54682473-54685646	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54681600-54682800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
2	chr2:54681800-54682600	Flanking Active TSS	Brain Anterior Caudate	brain
3	chr2:54681800-54682600	Flanking Active TSS	HSMMtube	muscle
4	chr2:54681800-54683200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:54682000-54682600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr2:54682000-54682800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:54682000-54683000	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr2:54682000-54685000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr2:54682000-54685400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr2:54682000-54685400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:54682000-54685600	Active TSS	Brain Substantia Nigra	brain
12	chr2:54682000-54686200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:54682200-54682600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr2:54682200-54682600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:54682200-54682600	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr2:54682200-54682600	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr2:54682200-54682600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr2:54682200-54682600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:54682200-54682600	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr2:54682200-54682600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
21	chr2:54682200-54682600	Flanking Active TSS	Fetal Brain Female	brain
22	chr2:54682200-54682600	Flanking Active TSS	Fetal Lung	lung
23	chr2:54682200-54682600	Active TSS	Pancreas	Pancrea
24	chr2:54682200-54682600	Active TSS	Rectal Smooth Muscle	rectum
25	chr2:54682200-54682600	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr2:54682200-54682800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:54682200-54682800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:54682200-54682800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:54682200-54682800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr2:54682200-54682800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:54682200-54682800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:54682200-54682800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
33	chr2:54682200-54682800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
34	chr2:54682200-54682800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:54682200-54682800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:54682200-54682800	Flanking Active TSS	Fetal Brain Male	brain
37	chr2:54682200-54682800	Flanking Active TSS	Fetal Stomach	stomach
38	chr2:54682200-54682800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr2:54682200-54682800	Bivalent/Poised TSS	Thymus	Thymus
40	chr2:54682200-54682800	Flanking Active TSS	NH-A	brain
41	chr2:54682200-54682800	Flanking Bivalent TSS/Enh	NHEK	skin
42	chr2:54682200-54683000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr2:54682200-54683000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr2:54682200-54683000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:54682200-54683000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:54682200-54683000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
47	chr2:54682200-54683000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr2:54682200-54683000	Flanking Active TSS	Fetal Muscle Trunk	muscle
49	chr2:54682200-54683000	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr2:54682200-54683000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum

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