Variant report

Variant	rs542150468
Chromosome Location	chr13:51796343-51796344
allele	-/CACGCGCTCGCA
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	CTCF	chr13:51796242-51796613	GM19238	blood:	n/a	n/a
2	PAX5	chr13:51796139-51796683	GM12892	blood:	n/a	n/a
3	MAX	chr13:51796039-51796406	A549	lung:	n/a	chr13:51796175-51796185
4	MAX	chr13:51796127-51796429	Hela-S3	cervix:	n/a	chr13:51796175-51796185
5	MYC	chr13:51795975-51796593	NB4	blood:	n/a	chr13:51796175-51796185
6	RAD21	chr13:51796343-51796592	SK-N-SH_RA	brain:	n/a	n/a
7	POLR2A	chr13:51796136-51796677	ECC-1	luminal epithelium:	n/a	n/a
8	MYC	chr13:51796059-51796358	H1-hESC	embryonic stem cell:	n/a	chr13:51796175-51796185
9	MAX	chr13:51796046-51796385	HepG2	liver:	n/a	chr13:51796175-51796185
10	CTCF	chr13:51796203-51796573	Gliobla	brain:	n/a	n/a
11	MAZ	chr13:51796296-51796572	K562	blood:	n/a	n/a
12	TCF12	chr13:51795966-51796405	A549	lung:	n/a	chr13:51795991-51795998
13	RAD21	chr13:51796308-51796674	SK-N-SH_RA	brain:	n/a	n/a
14	MAZ	chr13:51796102-51796961	IMR90	lung:	n/a	chr13:51796175-51796185
15	GTF2F1	chr13:51796233-51796461	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZNF263	chr13:51795947-51797402	HEK293-T-REx	kidney:	n/a	chr13:51796069-51796078 chr13:51797021-51797030 chr13:51796761-51796770
17	PAX5	chr13:51796252-51796585	GM12878	blood:	n/a	n/a
18	CREB1	chr13:51796185-51796795	A549	lung:	n/a	n/a
19	POLR2A	chr13:51796121-51796709	A549	lung:	n/a	n/a
20	MYC	chr13:51796093-51796417	MCF-7	breast:	n/a	chr13:51796175-51796185
21	MYC	chr13:51796026-51796511	MCF-7	breast:	n/a	chr13:51796175-51796185
22	MAX	chr13:51795936-51796601	HCT-116	colon:	n/a	chr13:51796175-51796185
23	POLR2A	chr13:51796174-51796747	HEK293	kidney:	n/a	n/a
24	CTCF	chr13:51796169-51797100	MCF-7	breast:	n/a	chr13:51797054-51797072 chr13:51796882-51796891
25	MYC	chr13:51796120-51796412	MCF-7	breast:	n/a	chr13:51796175-51796185
26	USF2	chr13:51796146-51796343	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr13:51796304-51796678	IMR90	lung:	n/a	n/a
28	NRF1	chr13:51795775-51796758	SK-N-SH	brain:	n/a	chr13:51796174-51796183
29	MYC	chr13:51795916-51796425	MCF10A-Er-Src	breast:	n/a	chr13:51796175-51796185
30	MAX	chr13:51795812-51796692	A549	lung:	n/a	chr13:51796175-51796185
31	POLR2A	chr13:51795999-51796422	HL-60	blood:	n/a	n/a
32	CTCF	chr13:51796340-51796490	NHDF-neo	bronchial:	n/a	n/a
33	TAF1	chr13:51796295-51796700	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr13:51795976-51796563	MCF-7	breast:	n/a	chr13:51796175-51796185
35	PAX5	chr13:51796085-51796382	GM12878	blood:	n/a	n/a
36	POLR2A	chr13:51796162-51796416	A549	lung:	n/a	n/a
37	MAX	chr13:51796212-51796412	K562	blood:	n/a	n/a
38	MYC	chr13:51796219-51796373	K562	blood:	n/a	n/a
39	CTCF	chr13:51795851-51797362	A549	lung:	n/a	chr13:51797054-51797072 chr13:51796882-51796891
40	NRF1	chr13:51796313-51796513	H1-hESC	embryonic stem cell:	n/a	n/a
41	E2F6	chr13:51796113-51796528	K562	blood:	n/a	chr13:51796174-51796183
42	MAX	chr13:51795916-51796690	H1-hESC	embryonic stem cell:	n/a	chr13:51796175-51796185
43	MAX	chr13:51795921-51796620	A549	lung:	n/a	chr13:51796175-51796185
44	POLR2A	chr13:51795993-51796772	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chr13:51796166-51796373	HCT-116	colon:	n/a	n/a
46	CTCF	chr13:51796173-51796611	MCF-7	breast:	n/a	n/a
47	RAD21	chr13:51796277-51796705	H1-hESC	embryonic stem cell:	n/a	n/a
48	MAX	chr13:51796025-51796876	HepG2	liver:	n/a	chr13:51796175-51796185
49	POLR2A	chr13:51796077-51796766	HUVEC	blood vessel:	n/a	n/a
50	PAX5	chr13:51796106-51796365	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SERPINE3-4	chr13:51795151-51798286	ncRnaDb_ncrna_FR376720_3

Variant related genes	Relation type
FAM124A	TF binding region

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832610	chr13:51636661-51822106	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv3332869	chr13:51795701-51797799	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr13:51795600-51796400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr13:51795600-51797200	Active TSS	A549	lung
3	chr13:51795800-51796400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:51795800-51796400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
5	chr13:51795800-51796400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr13:51795800-51796400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr13:51795800-51796400	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr13:51795800-51796400	Flanking Active TSS	Fetal Brain Male	brain
9	chr13:51795800-51796400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
10	chr13:51795800-51796400	Flanking Active TSS	Right Ventricle	heart
11	chr13:51795800-51796400	Flanking Bivalent TSS/Enh	Dnd41	blood
12	chr13:51795800-51796400	Flanking Bivalent TSS/Enh	HMEC	breast
13	chr13:51795800-51796400	Flanking Active TSS	HUVEC	blood vessel
14	chr13:51795800-51796400	Flanking Active TSS	NHLF	lung
15	chr13:51795800-51796600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:51795800-51796800	Active TSS	Stomach Smooth Muscle	stomach
17	chr13:51795800-51796800	Bivalent/Poised TSS	NHEK	skin
18	chr13:51795800-51797000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:51795800-51797000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:51795800-51797000	Bivalent/Poised TSS	GM12878-XiMat	blood
21	chr13:51795800-51797200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:51795800-51797400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr13:51795800-51797400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
24	chr13:51795800-51797400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr13:51795800-51797400	Bivalent/Poised TSS	Thymus	Thymus
26	chr13:51795800-51797600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr13:51795800-51797600	Active TSS	Brain Anterior Caudate	brain
28	chr13:51795800-51797600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
29	chr13:51795800-51797800	Active TSS	H1 Cell Line	embryonic stem cell
30	chr13:51795800-51797800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
31	chr13:51795800-51798000	Active TSS	Fetal Brain Female	brain
32	chr13:51795800-51798400	Active TSS	H9 Cell Line	embryonic stem cell
33	chr13:51795800-51798600	Active TSS	Brain Cingulate Gyrus	brain
34	chr13:51795800-51798800	Active TSS	Brain Hippocampus Middle	brain
35	chr13:51795800-51799000	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr13:51796000-51796400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:51796000-51796400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:51796000-51796400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr13:51796000-51796400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr13:51796000-51796400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr13:51796000-51796400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
42	chr13:51796000-51796400	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
43	chr13:51796000-51796400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr13:51796000-51796400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr13:51796000-51796400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:51796000-51796400	Flanking Active TSS	Liver	Liver
47	chr13:51796000-51796400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
48	chr13:51796000-51796400	Flanking Bivalent TSS/Enh	Placenta	Placenta
49	chr13:51796000-51796400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
50	chr13:51796000-51796400	Flanking Active TSS	Ovary	ovary

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