Variant report

Variant	rs546656076
Chromosome Location	chr3:49506492-49506493
allele	A/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	TEAD4	chr3:49506373-49507494	HepG2	liver:	n/a	n/a
6	CTCF	chr3:49506440-49506590	BJ	skin:	n/a	n/a
7	SIN3AK20	chr3:49506466-49507175	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr3:49506480-49506630	BJ	skin:	n/a	n/a
9	TEAD4	chr3:49506388-49507335	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr3:49506429-49507427	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:49506441-49508367	GM12878	blood:	n/a	n/a
12	CTCF	chr3:49506380-49506530	NHDF-neo	bronchial:	n/a	n/a
13	SMC3	chr3:49506446-49508398	Hela-S3	cervix:	n/a	chr3:49506615-49506622
14	NRF1	chr3:49506377-49508357	SK-N-SH	brain:	n/a	chr3:49507530-49507541
15	ELF1	chr3:49506485-49508399	GM12878	blood:	n/a	chr3:49508283-49508292 chr3:49507573-49507582 chr3:49508285-49508297
16	NFIC	chr3:49506384-49507078	ECC-1	luminal epithelium:	n/a	chr3:49506681-49506697 chr3:49506680-49506697
17	MAX	chr3:49506424-49508496	HepG2	liver:	n/a	chr3:49507013-49507023
18	TEAD4	chr3:49506489-49506965	A549	lung:	n/a	n/a
19	TEAD4	chr3:49506464-49506847	K562	blood:	n/a	n/a
20	POLR2A	chr3:49506455-49506500	HepG2	liver:	n/a	n/a
21	TEAD4	chr3:49506433-49507497	ECC-1	luminal epithelium:	n/a	n/a
22	RCOR1	chr3:49506445-49506615	K562	blood:	n/a	n/a
23	CEBPB	chr3:49506379-49508231	Hela-S3	cervix:	n/a	chr3:49507491-49507499
24	TFAP2C	chr3:49506472-49508405	Hela-S3	cervix:	n/a	chr3:49507037-49507052
25	CHD1	chr3:49506442-49506605	H1-hESC	embryonic stem cell:	n/a	n/a
26	TEAD4	chr3:49506417-49507172	K562	blood:	n/a	n/a
27	ZNF263	chr3:49506417-49508291	HEK293-T-REx	kidney:	n/a	n/a
28	MAX	chr3:49506400-49508424	HepG2	liver:	n/a	chr3:49507013-49507023
29	JUND	chr3:49506489-49507878	H1-hESC	embryonic stem cell:	n/a	chr3:49507492-49507501 chr3:49507236-49507245
30	POLR2A	chr3:49506351-49508245	SK-N-SH	brain:	n/a	n/a
31	TEAD4	chr3:49506429-49507447	H1-hESC	embryonic stem cell:	n/a	n/a
32	TEAD4	chr3:49506378-49508366	ECC-1	luminal epithelium:	n/a	n/a
33	CREB1	chr3:49506478-49508467	HepG2	liver:	n/a	n/a
34	POLR2A	chr3:49506311-49508860	H1-hESC	embryonic stem cell:	n/a	n/a
35	MXI1	chr3:49506448-49509224	IMR90	lung:	n/a	n/a
36	RCOR1	chr3:49506455-49508452	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr3:49506478-49508361	ECC-1	luminal epithelium:	n/a	n/a
38	SP1	chr3:49506382-49507859	H1-hESC	embryonic stem cell:	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
39	MAX	chr3:49506429-49508339	ECC-1	luminal epithelium:	n/a	chr3:49507013-49507023
40	MAZ	chr3:49506361-49509347	IMR90	lung:	n/a	chr3:49507013-49507023 chr3:49509096-49509107

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

Variant related genes	Relation type
RNA5SP130	TF binding region
DAG1	TF binding region
ENSG00000272434	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000235261	Chromatin interaction
ENSG00000201301	Chromatin interaction
ENSG00000145022	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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49490600-49506600	Enhancers	Fetal Muscle Leg	muscle
2	chr3:49499600-49506600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:49500000-49506600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:49501400-49506600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:49502200-49506600	Enhancers	Fetal Muscle Trunk	muscle
6	chr3:49502600-49506800	Enhancers	Fetal Heart	heart
7	chr3:49503000-49506600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:49503600-49506600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:49503600-49506600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:49503600-49507200	Weak transcription	Spleen	Spleen
11	chr3:49503800-49506600	Weak transcription	Esophagus	oesophagus
12	chr3:49503800-49506600	Weak transcription	Ovary	ovary
13	chr3:49504000-49506600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:49504000-49506600	Weak transcription	Fetal Intestine Small	intestine
15	chr3:49504000-49507000	Weak transcription	Small Intestine	intestine
16	chr3:49504800-49506800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:49505600-49506600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:49505600-49506600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:49505600-49506600	Enhancers	Pancreas	Pancrea
20	chr3:49505600-49507000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:49505600-49507000	Enhancers	Left Ventricle	heart
22	chr3:49505800-49506600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:49505800-49506600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:49505800-49506600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:49505800-49506600	Enhancers	Right Ventricle	heart
26	chr3:49505800-49507000	Enhancers	Stomach Mucosa	stomach
27	chr3:49506000-49506600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:49506000-49506600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:49506000-49506600	Enhancers	Fetal Lung	lung
30	chr3:49506000-49506800	Enhancers	Fetal Stomach	stomach
31	chr3:49506000-49507200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:49506000-49507400	Flanking Active TSS	Hela-S3	cervix
33	chr3:49506200-49506600	Enhancers	Adipose Nuclei	Adipose
34	chr3:49506200-49506600	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr3:49506200-49506600	Enhancers	A549	lung
36	chr3:49506200-49506600	Enhancers	K562	blood
37	chr3:49506200-49506600	Enhancers	NHLF	lung
38	chr3:49506200-49507400	Flanking Active TSS	Placenta	Placenta
39	chr3:49506200-49507400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr3:49506400-49506600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:49506400-49506600	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr3:49506400-49506600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:49506400-49506600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:49506400-49506600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:49506400-49506600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:49506400-49506600	Enhancers	Brain Anterior Caudate	brain
47	chr3:49506400-49506600	Enhancers	Brain Hippocampus Middle	brain
48	chr3:49506400-49506600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:49506400-49506600	Enhancers	Brain Substantia Nigra	brain
50	chr3:49506400-49506600	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links