Variant report

Variant	rs541685808
Chromosome Location	chr13:50510808-50510809
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	PAX5	chr13:50510184-50511022	GM12878	blood:	n/a	chr13:50510638-50510657
2	POLR2A	chr13:50510209-50510859	HCT-116	colon:	n/a	n/a
3	EP300	chr13:50510236-50510948	GM12878	blood:	n/a	n/a
4	RCOR1	chr13:50509909-50510883	HepG2	liver:	n/a	n/a
5	POLR2A	chr13:50509854-50510823	GM12878	blood:	n/a	n/a
6	MAX	chr13:50509736-50511178	SK-N-SH	brain:	n/a	chr13:50511019-50511028 chr13:50511016-50511027 chr13:50510651-50510661
7	POLR2A	chr13:50509769-50511260	GM12892	blood:	n/a	n/a
8	HDAC2	chr13:50509772-50510917	HepG2	liver:	n/a	n/a
9	POLR2A	chr13:50510202-50510918	HepG2	liver:	n/a	n/a
10	HCFC1	chr13:50509342-50511153	Hela-S3	cervix:	n/a	n/a
11	KAP1	chr13:50510089-50510933	HEK293	kidney:	n/a	n/a
12	PAX5	chr13:50510567-50510813	GM12878	blood:	n/a	chr13:50510638-50510657
13	USF2	chr13:50510438-50511138	GM12878	blood:	n/a	n/a
14	MXI1	chr13:50509251-50511503	SK-N-SH	brain:	n/a	n/a
15	CREB1	chr13:50510244-50510817	A549	lung:	n/a	n/a
16	POLR2A	chr13:50509686-50511055	U87	brain:	n/a	n/a
17	POLR2A	chr13:50509848-50511344	MCF-7	breast:	n/a	n/a
18	POLR2A	chr13:50510200-50511130	GM12892	blood:	n/a	n/a
19	ZBTB7A	chr13:50509867-50510839	K562	blood:	n/a	n/a
20	POLR2A	chr13:50510144-50511035	GM12891	blood:	n/a	n/a
21	SIN3AK20	chr13:50509830-50510965	H1-hESC	embryonic stem cell:	n/a	n/a
22	ETS1	chr13:50510248-50510885	GM12878	blood:	n/a	n/a
23	BHLHE40	chr13:50509964-50511018	HepG2	liver:	n/a	n/a
24	MAFK	chr13:50510352-50510823	HepG2	liver:	n/a	n/a
25	ELF1	chr13:50509822-50511477	GM12878	blood:	n/a	chr13:50510642-50510651
26	HCFC1	chr13:50510070-50510899	K562	blood:	n/a	n/a
27	NRF1	chr13:50510529-50510886	HepG2	liver:	n/a	chr13:50510639-50510648 chr13:50510696-50510710 chr13:50510693-50510707 chr13:50510696-50510707 chr13:50510696-50510707 chr13:50510698-50510707
28	POLR2A	chr13:50509622-50511072	K562	blood:	n/a	n/a
29	TAF1	chr13:50510694-50510841	GM12892	blood:	n/a	n/a
30	FOXM1	chr13:50510228-50510959	GM12878	blood:	n/a	n/a
31	ELF1	chr13:50510300-50510866	K562	blood:	n/a	chr13:50510642-50510651
32	POLR2A	chr13:50509838-50511315	GM19193	blood:	n/a	n/a
33	MAX	chr13:50509829-50511410	ECC-1	luminal epithelium:	n/a	chr13:50511019-50511028 chr13:50511016-50511027 chr13:50510651-50510661
34	PAX5	chr13:50510311-50510877	GM12878	blood:	n/a	chr13:50510638-50510657
35	PAX5	chr13:50510268-50511086	GM12878	blood:	n/a	chr13:50510638-50510657
36	SP1	chr13:50510198-50510838	A549	lung:	n/a	chr13:50510656-50510668 chr13:50510656-50510668 chr13:50510657-50510667 chr13:50510645-50510655 chr13:50510657-50510667
37	POLR2A	chr13:50509821-50510979	K562	blood:	n/a	n/a
38	CCNT2	chr13:50509871-50511160	K562	blood:	n/a	n/a
39	TAF1	chr13:50509693-50511193	ECC-1	luminal epithelium:	n/a	n/a
40	ZC3H11A	chr13:50510776-50510860	K562	blood:	n/a	n/a
41	CTCF	chr13:50509622-50511370	SK-N-SH	brain:	n/a	n/a
42	MAX	chr13:50509792-50510958	Hela-S3	cervix:	n/a	chr13:50510651-50510661
43	POLR2A	chr13:50509820-50510828	PFSK-1	brain:	n/a	n/a
44	MAX	chr13:50509845-50510919	H1-hESC	embryonic stem cell:	n/a	chr13:50510651-50510661
45	MYC	chr13:50510232-50510810	H1-hESC	embryonic stem cell:	n/a	chr13:50510651-50510661
46	MAX	chr13:50509797-50511198	K562	blood:	n/a	chr13:50511019-50511028 chr13:50511016-50511027 chr13:50510651-50510661
47	POLR2A	chr13:50510200-50510961	GM12892	blood:	n/a	n/a
48	ZNF143	chr13:50509966-50510910	H1-hESC	embryonic stem cell:	n/a	chr13:50510160-50510170
49	SIN3A	chr13:50509764-50511413	H1-hESC	embryonic stem cell:	n/a	chr13:50510961-50510974 chr13:50511018-50511027
50	RCOR1	chr13:50510046-50511136	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:50509071..50511034-chr13:50570092..50572951,3	K562	blood:
2	chr13:50509813..50511946-chr17:39844014..39846019,2	MCF-7	breast:
3	chr13:50365136..50367359-chr13:50509492..50511604,3	MCF-7	breast:
4	chr13:50510078..50512694-chr13:50569483..50571768,3	MCF-7	breast:
5	chr13:50510515..50512106-chr13:51482735..51485474,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM13-7	chr13:50510782-50513292	NONHSAT033768

Variant related genes	Relation type
SPRYD7	TF binding region
ENSG00000136104	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000233672	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1836423	chr13:50509784-50514706	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1836704	chr13:50509784-50514706	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1838605	chr13:50509784-50514706	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1834429	chr13:50509784-50536186	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50508800-50511400	Active TSS	Right Atrium	heart
2	chr13:50509000-50511400	Active TSS	A549	lung
3	chr13:50509000-50511400	Active TSS	K562	blood
4	chr13:50509000-50511600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:50509000-50511600	Active TSS	HMEC	breast
6	chr13:50509000-50511800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr13:50509200-50511400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:50509400-50511000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
9	chr13:50509400-50511200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:50509400-50511200	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr13:50509400-50511200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:50509400-50511200	Active TSS	Brain Hippocampus Middle	brain
13	chr13:50509400-50511200	Active TSS	Psoas Muscle	Psoas
14	chr13:50509400-50511400	Active TSS	H1 Cell Line	embryonic stem cell
15	chr13:50509400-50511400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr13:50509400-50511400	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr13:50509400-50511400	Active TSS	Fetal Intestine Large	intestine
18	chr13:50509400-50511400	Active TSS	HSMMtube	muscle
19	chr13:50509400-50511600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:50509400-50511600	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr13:50509400-50511600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:50509400-50511600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr13:50509400-50511600	Active TSS	NHLF	lung
24	chr13:50509600-50511000	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr13:50509600-50511000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr13:50509600-50511000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:50509600-50511000	Active TSS	Fetal Muscle Trunk	muscle
28	chr13:50509600-50511000	Active TSS	Placenta	Placenta
29	chr13:50509600-50511000	Active TSS	Hela-S3	cervix
30	chr13:50509600-50511200	Active TSS	Muscle Satellite Cultured Cells	--
31	chr13:50509600-50511200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr13:50509600-50511200	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr13:50509600-50511200	Active TSS	Fetal Lung	lung
34	chr13:50509600-50511200	Active TSS	Lung	lung
35	chr13:50509600-50511200	Active TSS	Stomach Mucosa	stomach
36	chr13:50509600-50511200	Active TSS	GM12878-XiMat	blood
37	chr13:50509600-50511400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:50509600-50511400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:50509600-50511400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr13:50509600-50511400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr13:50509600-50511400	Active TSS	Aorta	Aorta
42	chr13:50509600-50511400	Active TSS	Brain Cingulate Gyrus	brain
43	chr13:50509600-50511400	Active TSS	Esophagus	oesophagus
44	chr13:50509600-50511400	Active TSS	Left Ventricle	heart
45	chr13:50509600-50511400	Active TSS	Ovary	ovary
46	chr13:50509600-50511400	Active TSS	Pancreas	Pancrea
47	chr13:50509600-50511400	Active TSS	Placenta Amnion	Placenta Amnion
48	chr13:50509600-50511400	Active TSS	HepG2	liver
49	chr13:50509600-50511400	Active TSS	HSMM	muscle
50	chr13:50509600-50511400	Active TSS	NHDF-Ad	bronchial

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