Variant report

Variant	rs540408607
Chromosome Location	chr2:54681890-54681891
allele	C/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	CTCF	chr2:54681619-54681946	GM12878	blood:	n/a	n/a
3	RAD21	chr2:54681562-54682016	HepG2	liver:	n/a	chr2:54681763-54681770
4	FOXA1	chr2:54681217-54682489	HepG2	liver:	n/a	chr2:54681973-54681988 chr2:54681975-54681987
5	FOXA2	chr2:54681664-54682203	A549	lung:	n/a	chr2:54681975-54681987
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	HDAC2	chr2:54681601-54682052	HepG2	liver:	n/a	chr2:54681944-54681958 chr2:54681975-54681984 chr2:54681945-54681954
9	HNF4A	chr2:54681668-54682117	HepG2	liver:	n/a	n/a
10	RAD21	chr2:54681697-54681957	SK-N-SH_RA	brain:	n/a	chr2:54681763-54681770
11	HDAC2	chr2:54681564-54682156	HepG2	liver:	n/a	chr2:54681944-54681958 chr2:54681975-54681984 chr2:54681945-54681954
12	POLR2A	chr2:54681650-54683349	HepG2	liver:	n/a	n/a
13	FOXA1	chr2:54681590-54682475	HepG2	liver:	n/a	chr2:54681973-54681988 chr2:54681975-54681987
14	EP300	chr2:54681626-54682122	HepG2	liver:	n/a	chr2:54681670-54681680 chr2:54681974-54681984 chr2:54681743-54681753
15	NFIC	chr2:54681667-54682081	HepG2	liver:	n/a	n/a
16	FOXA2	chr2:54681127-54682857	HepG2	liver:	n/a	chr2:54681975-54681987
17	FOXA1	chr2:54681604-54682450	HepG2	liver:	n/a	chr2:54681973-54681988 chr2:54681975-54681987
18	ARID3A	chr2:54681591-54682242	HepG2	liver:	n/a	n/a
19	NFIC	chr2:54681500-54682550	HepG2	liver:	n/a	n/a
20	MXI1	chr2:54681837-54685789	SK-N-SH	brain:	n/a	n/a
21	RXRA	chr2:54681561-54682033	HepG2	liver:	n/a	n/a
22	MBD4	chr2:54681524-54682655	HepG2	liver:	n/a	n/a
23	EP300	chr2:54681611-54682171	HepG2	liver:	n/a	chr2:54681670-54681680 chr2:54681974-54681984 chr2:54681743-54681753
24	FOXA2	chr2:54681575-54682404	HepG2	liver:	n/a	chr2:54681975-54681987
25	CTCF	chr2:54681760-54681910	HCPEpiC	choroid plexus:	n/a	n/a
26	SP1	chr2:54681581-54682110	HepG2	liver:	n/a	n/a
27	RAD21	chr2:54681653-54681964	Hela-S3	cervix:	n/a	chr2:54681763-54681770
28	TEAD4	chr2:54681509-54682622	HepG2	liver:	n/a	n/a
29	FOXA1	chr2:54681521-54682299	HepG2	liver:	n/a	chr2:54681973-54681988 chr2:54681975-54681987

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

Variant related genes	Relation type
SPTBN1	TF binding region

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	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	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
7	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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54668600-54682000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:54677600-54682200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:54678600-54682200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:54681000-54682000	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:54681200-54682000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr2:54681200-54682200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:54681200-54682200	Enhancers	Liver	Liver
8	chr2:54681400-54682000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
9	chr2:54681400-54682000	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr2:54681400-54682200	Enhancers	Brain Hippocampus Middle	brain
11	chr2:54681600-54682000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr2:54681600-54682000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr2:54681600-54682000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
14	chr2:54681600-54682000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:54681600-54682000	Enhancers	Adipose Nuclei	Adipose
16	chr2:54681600-54682200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:54681600-54682200	Enhancers	Primary hematopoietic stem cells	blood
18	chr2:54681600-54682200	Enhancers	Brain Cingulate Gyrus	brain
19	chr2:54681600-54682200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr2:54681600-54682200	Enhancers	Fetal Heart	heart
21	chr2:54681600-54682800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
22	chr2:54681800-54682000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr2:54681800-54682000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:54681800-54682000	Enhancers	Brain Substantia Nigra	brain
25	chr2:54681800-54682000	Flanking Active TSS	Fetal Lung	lung
26	chr2:54681800-54682000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:54681800-54682000	Flanking Active TSS	A549	lung
28	chr2:54681800-54682200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
29	chr2:54681800-54682200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:54681800-54682200	Enhancers	Brain Angular Gyrus	brain
31	chr2:54681800-54682200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:54681800-54682200	Enhancers	Fetal Brain Male	brain
33	chr2:54681800-54682200	Bivalent Enhancer	Fetal Intestine Small	intestine
34	chr2:54681800-54682200	Enhancers	Fetal Kidney	kidney
35	chr2:54681800-54682200	Active TSS	HepG2	liver
36	chr2:54681800-54682200	Enhancers	HUVEC	blood vessel
37	chr2:54681800-54682400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:54681800-54682600	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr2:54681800-54682600	Flanking Active TSS	HSMMtube	muscle
40	chr2:54681800-54683200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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