Variant report

Variant	rs562762546
Chromosome Location	chr13:96329398-96329399
allele	A/C
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	POLR2A	chr13:96328335-96330029	GM18526	blood:	n/a	n/a
2	REST	chr13:96328754-96329704	H1-neurons	neurons:	n/a	chr13:96329358-96329371
3	SPI1	chr13:96328874-96329859	HL-60	blood:	n/a	chr13:96329375-96329382
4	POLR2A	chr13:96328328-96329699	GM12878	blood:	n/a	n/a
5	POLR2A	chr13:96328334-96329690	GM12878	blood:	n/a	n/a
6	TBL1XR1	chr13:96328771-96329503	K562	blood:	n/a	n/a
7	POU2F2	chr13:96328807-96329739	GM12878	blood:	n/a	chr13:96329362-96329374
8	MXI1	chr13:96328102-96331205	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr13:96327871-96330548	PBDE	blood:	n/a	n/a
10	SP1	chr13:96328788-96329617	A549	lung:	n/a	chr13:96329232-96329243 chr13:96329358-96329368 chr13:96329234-96329243 chr13:96329358-96329367 chr13:96329234-96329243 chr13:96329232-96329244 chr13:96329358-96329368 chr13:96329232-96329244 chr13:96329359-96329368 chr13:96329229-96329243 chr13:96329357-96329369 chr13:96329357-96329369 chr13:96329233-96329242
11	ELF1	chr13:96329263-96329992	SK-N-SH	brain:	n/a	chr13:96329325-96329334 chr13:96329790-96329802 chr13:96329359-96329371 chr13:96329352-96329364
12	MYC	chr13:96329346-96329512	K562	blood:	n/a	chr13:96329358-96329368
13	POLR2A	chr13:96328287-96330029	K562	blood:	n/a	n/a
14	MAX	chr13:96328443-96329873	HCT-116	colon:	n/a	chr13:96329358-96329368
15	POLR2A	chr13:96329307-96329558	H1-hESC	embryonic stem cell:	n/a	n/a
16	TCF3	chr13:96329286-96329568	GM12878	blood:	n/a	n/a
17	USF2	chr13:96329024-96329462	GM12878	blood:	n/a	chr13:96329181-96329197 chr13:96329427-96329443 chr13:96329435-96329451
18	SP1	chr13:96328936-96329606	H1-hESC	embryonic stem cell:	n/a	chr13:96329232-96329243 chr13:96329358-96329368 chr13:96329234-96329243 chr13:96329358-96329367 chr13:96329234-96329243 chr13:96329232-96329244 chr13:96329358-96329368 chr13:96329232-96329244 chr13:96329359-96329368 chr13:96329229-96329243 chr13:96329357-96329369 chr13:96329357-96329369 chr13:96329233-96329242
19	CREB1	chr13:96328202-96329895	HepG2	liver:	n/a	n/a
20	POLR2A	chr13:96328065-96329699	K562	blood:	n/a	n/a
21	YY1	chr13:96328992-96329710	ECC-1	luminal epithelium:	n/a	chr13:96329245-96329259 chr13:96329599-96329610 chr13:96329451-96329465 chr13:96329357-96329371 chr13:96329185-96329199 chr13:96329241-96329250 chr13:96329325-96329334 chr13:96329241-96329255
22	POLR2A	chr13:96328855-96329648	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr13:96328315-96330194	NB4	blood:	n/a	n/a
24	IRF1	chr13:96328182-96329594	K562	blood:	n/a	chr13:96329355-96329369 chr13:96329232-96329246
25	E2F6	chr13:96328742-96329740	A549	lung:	n/a	chr13:96329449-96329458 chr13:96329239-96329249
26	SIN3AK20	chr13:96329300-96329636	A549	lung:	n/a	n/a
27	TAF1	chr13:96328974-96329668	GM12891	blood:	n/a	n/a
28	REST	chr13:96328205-96329839	HL-60	blood:	n/a	chr13:96329792-96329805 chr13:96329358-96329371
29	E2F6	chr13:96328923-96329739	K562	blood:	n/a	chr13:96329449-96329458 chr13:96329239-96329249
30	SP4	chr13:96329045-96329638	H1-hESC	embryonic stem cell:	n/a	chr13:96329232-96329243 chr13:96329357-96329373 chr13:96329355-96329371
31	POLR2A	chr13:96328823-96329864	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr13:96328695-96329808	MCF-7	breast:	n/a	n/a
33	ZKSCAN1	chr13:96328372-96329916	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr13:96327780-96329630	K562	blood:	n/a	n/a
35	POLR2A	chr13:96328269-96330465	GM12891	blood:	n/a	n/a
36	CHD2	chr13:96328430-96329733	GM12878	blood:	n/a	chr13:96329234-96329244
37	POLR2A	chr13:96328328-96329653	K562	blood:	n/a	n/a
38	IRF1	chr13:96328759-96329636	K562	blood:	n/a	chr13:96329355-96329369 chr13:96329615-96329624 chr13:96329232-96329246
39	RELA	chr13:96328398-96329610	GM19099	blood:	n/a	n/a
40	RCOR1	chr13:96328716-96329519	K562	blood:	n/a	n/a
41	UBTF	chr13:96328690-96330213	K562	blood:	n/a	n/a
42	HMGN3	chr13:96328963-96329922	K562	blood:	n/a	n/a
43	POLR2A	chr13:96328734-96329963	MCF-7	breast:	n/a	n/a
44	REST	chr13:96328809-96329676	HepG2	liver:	n/a	chr13:96329358-96329371
45	YY1	chr13:96328979-96329798	GM12891	blood:	n/a	chr13:96329783-96329797 chr13:96329245-96329259 chr13:96329599-96329610 chr13:96329451-96329465 chr13:96329357-96329371 chr13:96329185-96329199 chr13:96329241-96329250 chr13:96329786-96329795 chr13:96329325-96329334 chr13:96329241-96329255
46	ELF1	chr13:96328928-96329803	MCF-7	breast:	n/a	chr13:96329325-96329334 chr13:96329790-96329802 chr13:96329359-96329371 chr13:96329352-96329364 chr13:96329243-96329255 chr13:96329186-96329198
47	MAFK	chr13:96329386-96329481	HepG2	liver:	n/a	n/a
48	BCLAF1	chr13:96328727-96329765	GM12878	blood:	n/a	chr13:96329241-96329254 chr13:96329237-96329250 chr13:96329321-96329334 chr13:96329326-96329335 chr13:96329424-96329437 chr13:96329239-96329248 chr13:96329712-96329725 chr13:96329186-96329199
49	TAF7	chr13:96328631-96329729	H1-hESC	embryonic stem cell:	n/a	n/a
50	MYC	chr13:96328275-96330568	NB4	blood:	n/a	chr13:96329358-96329368

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:96329351-96329401	MCF10A-Er-Src	breast:	n/a
2	chr13:96329362-96329412	AG09309	skin:	n/a
3	chr13:96329362-96329412	SKMC	muscle:	n/a
4	chr13:96329351-96329401	AG09319	gingival:	n/a
5	chr13:96329362-96329412	Hela-S3	cervix:	n/a
6	chr13:96329362-96329412	LNCaP	prostate:	n/a
7	chr13:96329362-96329412	GM19239	blood:	n/a
8	chr13:96329351-96329401	ECC-1	luminal epithelium:	n/a
9	chr13:96329351-96329401	MCF-7	breast:	n/a
10	chr13:96329355-96329405	K562	blood:	n/a
11	chr13:96329351-96329401	H1-hESC	embryonic stem cell:	embryo
12	chr13:96329362-96329412	NHDF-neo	bronchial:	n/a
13	chr13:96329351-96329401	GM12891	blood:	n/a
14	chr13:96329351-96329401	HCT-116	colon:	n/a
15	chr13:96329362-96329412	AoSMC	blood vessel:	n/a
16	chr13:96329351-96329401	SKMC	muscle:	n/a
17	chr13:96329355-96329405	U87	brain:	n/a
18	chr13:96329355-96329405	PrEC	prostate:	n/a
19	chr13:96329362-96329412	PFSK-1	brain:	n/a
20	chr13:96329351-96329401	HEEpiC	esophagus:	n/a
21	chr13:96329355-96329405	IMR90	lung:	fetal
22	chr13:96329351-96329401	AG04449	skin:	fetal
23	chr13:96329355-96329405	ProgFib	skin:	n/a
24	chr13:96329362-96329412	HPAEpiC	pulmonary alveolar:	n/a
25	chr13:96329355-96329405	HRCEpiC	kidney:	n/a
26	chr13:96329362-96329412	MCF10A-Er-Src	breast:	n/a
27	chr13:96329362-96329412	MCF-7	breast:	n/a
28	chr13:96329355-96329405	LNCaP	prostate:	n/a
29	chr13:96329351-96329401	NHDF-neo	bronchial:	n/a
30	chr13:96329351-96329401	HIPEpiC	eye:	n/a
31	chr13:96329355-96329405	A549	lung:	n/a
32	chr13:96329362-96329412	HEEpiC	esophagus:	n/a
33	chr13:96329355-96329405	SAEC	small airway:	n/a
34	chr13:96329362-96329412	AG04449	skin:	fetal
35	chr13:96329355-96329405	HCF	heart:	n/a
36	chr13:96329355-96329405	HL-60	blood:	n/a
37	chr13:96329351-96329401	HPAEpiC	pulmonary alveolar:	n/a
38	chr13:96329351-96329401	ProgFib	skin:	n/a
39	chr13:96329351-96329401	K562	blood:	n/a
40	chr13:96329355-96329405	NHDF-neo	bronchial:	n/a
41	chr13:96329362-96329412	HCF	heart:	n/a
42	chr13:96329351-96329401	RPTEC	kidney:	n/a
43	chr13:96329355-96329405	HCPEpiC	choroid plexus:	n/a
44	chr13:96329355-96329405	CMK	blood:	n/a
45	chr13:96329362-96329412	NB4	blood:	n/a
46	chr13:96329355-96329405	GM12891	blood:	n/a
47	chr13:96329355-96329405	GM12878	blood:	n/a
48	chr13:96329355-96329405	HUVEC	blood vessel:	n/a
49	chr13:96329362-96329412	RPTEC	kidney:	n/a
50	chr13:96329355-96329405	MCF-7	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65190165..65191035-chr13:96328786..96329458,2	Hela-S3	cervix:
2	chr13:96329295..96329836-chr16:31470265..31470990,2	Hela-S3	cervix:
3	chr13:96328903..96329487-chr15:42565285..42566134,2	Hela-S3	cervix:
4	chr13:96328782..96329500-chr7:138793896..138794495,2	Hela-S3	cervix:
5	chr13:96329134..96329884-chr14:91526708..91527516,2	NB4	blood:
6	chr13:96329213..96330784-chr13:96346091..96348298,2	MCF-7	breast:
7	chr13:96327826..96331109-chr13:96365382..96368282,3	MCF-7	breast:
8	chr13:96328671..96329561-chr2:64680996..64681548,2	Hela-S3	cervix:
9	chr13:96327692..96330287-chr13:96346205..96350903,4	K562	blood:

Variant related genes	Relation type
DNAJC3	TF binding region
DNAJC3-AS1	TF binding region
DNAJC3	CpG island
DNAJC3-AS1	CpG island
ENSG00000100784	Chromatin interaction
ENSG00000105939	Chromatin interaction
ENSG00000214013	Chromatin interaction
ENSG00000119862	Chromatin interaction
ENSG00000133943	Chromatin interaction
ENSG00000103978	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000227714	Chromatin interaction
ENSG00000251901	Chromatin interaction
ENSG00000232373	Chromatin interaction
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 1 )
Associated
traits (count: 0)

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3406527	chr13:96328176-96330724	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96325600-96332400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:96327000-96330600	Active TSS	Duodenum Mucosa	Duodenum
3	chr13:96327000-96330800	Active TSS	Fetal Intestine Large	intestine
4	chr13:96327000-96331000	Active TSS	K562	blood
5	chr13:96327000-96331800	Active TSS	GM12878-XiMat	blood
6	chr13:96327200-96331000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr13:96327400-96331000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr13:96327600-96329400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:96327600-96330000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr13:96327600-96330400	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr13:96327600-96330600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:96327600-96330800	Active TSS	Fetal Intestine Small	intestine
13	chr13:96327600-96331000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr13:96327600-96331000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:96327600-96331000	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr13:96327600-96331000	Active TSS	HMEC	breast
17	chr13:96327600-96331200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr13:96327600-96331400	Active TSS	Right Ventricle	heart
19	chr13:96327800-96329400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr13:96327800-96331000	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr13:96328000-96330200	Active TSS	Brain Anterior Caudate	brain
22	chr13:96328000-96330200	Active TSS	Fetal Brain Female	brain
23	chr13:96328000-96330400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:96328000-96330600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr13:96328000-96330600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr13:96328000-96330600	Active TSS	Psoas Muscle	Psoas
27	chr13:96328000-96330600	Active TSS	Stomach Smooth Muscle	stomach
28	chr13:96328000-96330800	Active TSS	H1 Cell Line	embryonic stem cell
29	chr13:96328000-96330800	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr13:96328000-96330800	Active TSS	NHEK	skin
31	chr13:96328000-96331000	Active TSS	Colon Smooth Muscle	Colon
32	chr13:96328000-96331000	Active TSS	A549	lung
33	chr13:96328000-96331000	Active TSS	Hela-S3	cervix
34	chr13:96328000-96331000	Active TSS	HSMMtube	muscle
35	chr13:96328000-96331200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:96328000-96331200	Active TSS	Colonic Mucosa	Colon
37	chr13:96328000-96331200	Active TSS	Ovary	ovary
38	chr13:96328000-96332000	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr13:96328200-96329400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr13:96328200-96329600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:96328200-96330000	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr13:96328200-96330000	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr13:96328200-96330000	Active TSS	Fetal Thymus	thymus
44	chr13:96328200-96330200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr13:96328200-96330200	Active TSS	Thymus	Thymus
46	chr13:96328200-96330400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr13:96328200-96330400	Active TSS	Liver	Liver
48	chr13:96328200-96330600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr13:96328200-96330600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr13:96328200-96330600	Active TSS	H9 Cell Line	embryonic stem cell

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