Variant report

Variant	rs540074560
Chromosome Location	chr3:49506732-49506733
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	MXI1	chr3:49506252-49509681	SK-N-SH	brain:	n/a	n/a
2	MAX	chr3:49506483-49508246	SK-N-SH	brain:	n/a	chr3:49507013-49507023
3	MAX	chr3:49506406-49508265	A549	lung:	n/a	chr3:49507013-49507023
4	NFIC	chr3:49506364-49507381	ECC-1	luminal epithelium:	n/a	chr3:49506681-49506697 chr3:49506680-49506697
5	ZBTB7A	chr3:49506706-49507079	K562	blood:	n/a	n/a
6	TEAD4	chr3:49506373-49507494	HepG2	liver:	n/a	n/a
7	SP1	chr3:49506683-49507734	A549	lung:	n/a	chr3:49507515-49507527 chr3:49507353-49507362 chr3:49507015-49507029 chr3:49507515-49507527 chr3:49507351-49507363 chr3:49507672-49507681 chr3:49507019-49507028 chr3:49507516-49507525 chr3:49507479-49507489 chr3:49507517-49507526 chr3:49507352-49507366 chr3:49507479-49507489 chr3:49507352-49507361 chr3:49507671-49507683 chr3:49507671-49507683 chr3:49507352-49507362 chr3:49507018-49507030 chr3:49507489-49507510 chr3:49507351-49507363 chr3:49507517-49507526
8	POLR2A	chr3:49506564-49508420	K562	blood:	n/a	n/a
9	RFX5	chr3:49506541-49508416	Hela-S3	cervix:	n/a	chr3:49507491-49507500 chr3:49507276-49507285 chr3:49507650-49507664 chr3:49507647-49507662 chr3:49507651-49507660 chr3:49507649-49507665 chr3:49507648-49507662
10	SIN3AK20	chr3:49506466-49507175	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:49506704-49506889	Gliobla	brain:	n/a	n/a
12	TEAD4	chr3:49506388-49507335	SK-N-SH	brain:	n/a	n/a
13	TEAD4	chr3:49506429-49507427	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3A	chr3:49506507-49508607	H1-hESC	embryonic stem cell:	n/a	chr3:49507507-49507520 chr3:49506954-49506963 chr3:49507546-49507557
15	POLR2A	chr3:49506441-49508367	GM12878	blood:	n/a	n/a
16	SMC3	chr3:49506446-49508398	Hela-S3	cervix:	n/a	chr3:49506615-49506622
17	RAD21	chr3:49506605-49507204	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAFK	chr3:49506696-49507975	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr3:49506503-49508428	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:49506510-49508430	HepG2	liver:	n/a	n/a
21	NRF1	chr3:49506377-49508357	SK-N-SH	brain:	n/a	chr3:49507530-49507541
22	ELF1	chr3:49506485-49508399	GM12878	blood:	n/a	chr3:49508283-49508292 chr3:49507573-49507582 chr3:49508285-49508297
23	NFIC	chr3:49506384-49507078	ECC-1	luminal epithelium:	n/a	chr3:49506681-49506697 chr3:49506680-49506697
24	POLR2A	chr3:49506499-49506817	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr3:49506646-49508326	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr3:49506717-49508277	K562	blood:	n/a	n/a
27	MAX	chr3:49506424-49508496	HepG2	liver:	n/a	chr3:49507013-49507023
28	MAX	chr3:49506554-49508276	SK-N-SH	brain:	n/a	chr3:49507013-49507023
29	MAX	chr3:49506513-49508204	A549	lung:	n/a	chr3:49507013-49507023
30	POLR2A	chr3:49506582-49508385	MCF-7	breast:	n/a	n/a
31	TFAP2A	chr3:49506533-49507653	Hela-S3	cervix:	n/a	chr3:49507572-49507584 chr3:49507039-49507049 chr3:49507039-49507049 chr3:49507037-49507052
32	KAP1	chr3:49506659-49507419	U2OS	brain:	n/a	n/a
33	RCOR1	chr3:49506525-49508730	IMR90	lung:	n/a	n/a
34	TEAD4	chr3:49506489-49506965	A549	lung:	n/a	n/a
35	POLR2A	chr3:49506541-49508296	HCT-116	colon:	n/a	n/a
36	TEAD4	chr3:49506464-49506847	K562	blood:	n/a	n/a
37	GTF2F1	chr3:49506553-49507518	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:49506556-49508268	HCT-116	colon:	n/a	n/a
39	POLR2A	chr3:49506665-49508373	MCF-7	breast:	n/a	n/a
40	TAF1	chr3:49506571-49508366	H1-hESC	embryonic stem cell:	n/a	n/a
41	HEY1	chr3:49506646-49508236	HepG2	liver:	n/a	chr3:49507511-49507526 chr3:49507522-49507537 chr3:49507665-49507680 chr3:49508020-49508035 chr3:49507663-49507678 chr3:49507530-49507545
42	TEAD4	chr3:49506433-49507497	ECC-1	luminal epithelium:	n/a	n/a
43	EP300	chr3:49506652-49507354	A549	lung:	n/a	n/a
44	EP300	chr3:49506643-49508245	ECC-1	luminal epithelium:	n/a	chr3:49507533-49507549 chr3:49507573-49507582
45	CEBPB	chr3:49506379-49508231	Hela-S3	cervix:	n/a	chr3:49507491-49507499
46	CTCF	chr3:49506660-49506810	HCM	heart:	n/a	n/a
47	MYC	chr3:49506683-49506737	HUVEC	blood vessel:	n/a	n/a
48	SMARCB1	chr3:49506528-49508335	Hela-S3	cervix:	n/a	n/a
49	TFAP2C	chr3:49506472-49508405	Hela-S3	cervix:	n/a	chr3:49507037-49507052
50	TAF7	chr3:49506695-49508363	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49506494..49510419-chr3:49709515..49713189,4	MCF-7	breast:
2	chr3:49506481..49509131-chr3:49546764..49549304,2	MCF-7	breast:
3	chr3:49447402..49451449-chr3:49505916..49509646,7	K562	blood:
4	chr3:49506444..49509653-chr3:49710909..49714606,3	K562	blood:
5	chr3:49056423..49060378-chr3:49506507..49510634,4	K562	blood:
6	chr3:49447402..49452044-chr3:49506038..49509646,9	K562	blood:
7	chr3:49505441..49508480-chr3:49710122..49713377,5	MCF-7	breast:
8	chr3:49501861..49505109-chr3:49505439..49508808,5	K562	blood:
9	chr3:49448236..49450769-chr3:49505936..49509558,3	MCF-7	breast:
10	chr3:49460325..49461920-chr3:49506460..49509220,2	MCF-7	breast:
11	chr3:49043383..49045852-chr3:49505855..49507402,2	MCF-7	breast:
12	chr3:49503012..49504721-chr3:49506646..49509185,2	MCF-7	breast:
13	chr3:49065352..49067075-chr3:49506284..49508355,2	K562	blood:

Variant related genes	Relation type
DAG1	TF binding region
RNA5SP130	TF binding region
ENSG00000178057	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000235261	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000201301	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000164062	Chromatin interaction

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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3420339	chr3:49505548-49510046	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv3439400	chr3:49506373-49508921	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49502600-49506800	Enhancers	Fetal Heart	heart
2	chr3:49503600-49507200	Weak transcription	Spleen	Spleen
3	chr3:49504000-49507000	Weak transcription	Small Intestine	intestine
4	chr3:49504800-49506800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:49505600-49507000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:49505600-49507000	Enhancers	Left Ventricle	heart
7	chr3:49505800-49507000	Enhancers	Stomach Mucosa	stomach
8	chr3:49506000-49506800	Enhancers	Fetal Stomach	stomach
9	chr3:49506000-49507200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:49506000-49507400	Flanking Active TSS	Hela-S3	cervix
11	chr3:49506200-49507400	Flanking Active TSS	Placenta	Placenta
12	chr3:49506200-49507400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr3:49506400-49506800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:49506400-49506800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:49506400-49506800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr3:49506400-49506800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:49506400-49506800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:49506400-49506800	Enhancers	Liver	Liver
19	chr3:49506400-49506800	Enhancers	Brain Cingulate Gyrus	brain
20	chr3:49506400-49506800	Enhancers	Brain Germinal Matrix	brain
21	chr3:49506400-49506800	Enhancers	Gastric	stomach
22	chr3:49506400-49506800	Enhancers	Right Atrium	heart
23	chr3:49506400-49507000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:49506400-49507000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:49506400-49507000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:49506400-49507000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr3:49506400-49507000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr3:49506400-49507000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:49506400-49507000	Enhancers	Fetal Intestine Large	intestine
30	chr3:49506400-49507000	Enhancers	Fetal Thymus	thymus
31	chr3:49506400-49507000	Enhancers	Lung	lung
32	chr3:49506400-49507000	Enhancers	Placenta Amnion	Placenta Amnion
33	chr3:49506400-49507000	Flanking Active TSS	HepG2	liver
34	chr3:49506400-49507000	Enhancers	HUVEC	blood vessel
35	chr3:49506400-49507200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:49506400-49507200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr3:49506400-49507200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:49506400-49507200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:49506400-49507200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr3:49506400-49507200	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr3:49506400-49507400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:49506400-49507400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:49506400-49507400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:49506400-49507400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:49506400-49507400	Flanking Active TSS	Colonic Mucosa	Colon
46	chr3:49506400-49507400	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr3:49506400-49507400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr3:49506400-49507400	Flanking Active TSS	HSMMtube	muscle
49	chr3:49506400-49507600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:49506400-49507600	Flanking Active TSS	Stomach Smooth Muscle	stomach

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