Variant report

Variant	rs560425719
Chromosome Location	chr2:54682630-54682631
allele	C/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	MYBL2	chr2:54681501-54683343	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:54682588-54683692	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:54682189-54685375	H1-neurons	neurons:	n/a	n/a
4	MYBL2	chr2:54681631-54683715	HepG2	liver:	n/a	n/a
5	HEY1	chr2:54681566-54683738	HepG2	liver:	n/a	chr2:54683583-54683598 chr2:54683492-54683507
6	POLR2A	chr2:54682165-54683785	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:54682183-54682651	HepG2	liver:	n/a	n/a
8	TCF12	chr2:54682609-54683757	A549	lung:	n/a	n/a
9	POLR2A	chr2:54682488-54682817	MCF-7	breast:	n/a	n/a
10	POLR2A	chr2:54681650-54683349	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:54682611-54682636	A549	lung:	n/a	n/a
12	TAF1	chr2:54682217-54682844	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTBP2	chr2:54682379-54685140	H1-hESC	embryonic stem cell:	n/a	n/a
14	MBD4	chr2:54682085-54683332	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:54682190-54682676	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:54682360-54682660	Gliobla	brain:	n/a	n/a
17	FOXA2	chr2:54681127-54682857	HepG2	liver:	n/a	chr2:54681975-54681987
18	USF1	chr2:54682272-54682631	H1-hESC	embryonic stem cell:	n/a	chr2:54682429-54682440
19	MXI1	chr2:54682590-54684279	HepG2	liver:	n/a	n/a
20	MXI1	chr2:54681837-54685789	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr2:54682503-54682778	MCF-7	breast:	n/a	n/a
22	MBD4	chr2:54681524-54682655	HepG2	liver:	n/a	n/a
23	MAZ	chr2:54682047-54685233	IMR90	lung:	n/a	chr2:54682934-54682942 chr2:54683800-54683809 chr2:54682429-54682440
24	TAF1	chr2:54682113-54683746	H1-neurons	neurons:	n/a	n/a
25	YY1	chr2:54682200-54682817	HepG2	liver:	n/a	chr2:54682584-54682595 chr2:54682359-54682371
26	POLR2A	chr2:54682284-54683990	HepG2	liver:	n/a	n/a
27	HEY1	chr2:54681893-54683353	HepG2	liver:	n/a	n/a
28	YY1	chr2:54682129-54683355	H1-hESC	embryonic stem cell:	n/a	chr2:54683188-54683199 chr2:54682584-54682595 chr2:54682359-54682371
29	REST	chr2:54681921-54685572	H1-neurons	neurons:	n/a	chr2:54683922-54683942 chr2:54684871-54684881 chr2:54683744-54683757
30	POLR2A	chr2:54682123-54685349	H1-neurons	neurons:	n/a	n/a
31	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
32	NFIC	chr2:54682232-54683121	HepG2	liver:	n/a	n/a
33	MAX	chr2:54682088-54685404	A549	lung:	n/a	chr2:54682934-54682942 chr2:54683800-54683809 chr2:54682429-54682440
34	MAX	chr2:54682114-54685282	HepG2	liver:	n/a	chr2:54682934-54682942 chr2:54683800-54683809 chr2:54682429-54682440
35	POLR2A	chr2:54682445-54682662	HepG2	liver:	n/a	n/a
36	POLR2A	chr2:54682174-54683690	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:54682360-54682666	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAFF	chr2:54682571-54682699	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:124 , 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	chr2:54681800-54683200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:54682000-54682800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:54682000-54683000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr2:54682000-54685000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr2:54682000-54685400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr2:54682000-54685400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr2:54682000-54685600	Active TSS	Brain Substantia Nigra	brain
9	chr2:54682000-54686200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr2:54682200-54682800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:54682200-54682800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:54682200-54682800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:54682200-54682800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:54682200-54682800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:54682200-54682800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:54682200-54682800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
17	chr2:54682200-54682800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
18	chr2:54682200-54682800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:54682200-54682800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:54682200-54682800	Flanking Active TSS	Fetal Brain Male	brain
21	chr2:54682200-54682800	Flanking Active TSS	Fetal Stomach	stomach
22	chr2:54682200-54682800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr2:54682200-54682800	Bivalent/Poised TSS	Thymus	Thymus
24	chr2:54682200-54682800	Flanking Active TSS	NH-A	brain
25	chr2:54682200-54682800	Flanking Bivalent TSS/Enh	NHEK	skin
26	chr2:54682200-54683000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr2:54682200-54683000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr2:54682200-54683000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:54682200-54683000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:54682200-54683000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
31	chr2:54682200-54683000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr2:54682200-54683000	Flanking Active TSS	Fetal Muscle Trunk	muscle
33	chr2:54682200-54683000	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr2:54682200-54683000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
35	chr2:54682200-54683000	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr2:54682200-54683000	Flanking Active TSS	A549	lung
37	chr2:54682200-54683000	Flanking Active TSS	HUVEC	blood vessel
38	chr2:54682200-54683000	Flanking Active TSS	Osteobl	bone
39	chr2:54682200-54683200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr2:54682200-54683200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr2:54682200-54683200	Flanking Active TSS	Liver	Liver
42	chr2:54682200-54683200	Bivalent/Poised TSS	HepG2	liver
43	chr2:54682200-54685000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:54682200-54685200	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr2:54682200-54685400	Active TSS	H9 Cell Line	embryonic stem cell
46	chr2:54682200-54685400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:54682200-54685600	Active TSS	Fetal Kidney	kidney
48	chr2:54682200-54685800	Active TSS	Brain Germinal Matrix	brain
49	chr2:54682200-54686000	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr2:54682200-54686200	Active TSS	Left Ventricle	heart

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