Variant report

Variant	rs554953764
Chromosome Location	chr5:37839794-37839795
allele	-/CCG
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	chr5:37839792-37840931	IMR90	lung:	n/a	n/a
2	CTBP2	chr5:37839040-37840731	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr5:37839598-37840171	H1-hESC	embryonic stem cell:	n/a	chr5:37839794-37839804 chr5:37839800-37839810 chr5:37839797-37839807 chr5:37839877-37839887
4	SIN3A	chr5:37839736-37840035	H1-hESC	embryonic stem cell:	n/a	chr5:37839936-37839947 chr5:37839936-37839949
5	MAX	chr5:37839743-37840858	A549	lung:	n/a	chr5:37840289-37840299
6	MAX	chr5:37838109-37839800	H1-hESC	embryonic stem cell:	n/a	chr5:37839592-37839602 chr5:37839378-37839388 chr5:37839135-37839145
7	ZNF263	chr5:37839746-37841001	HEK293-T-REx	kidney:	n/a	chr5:37840249-37840258
8	SUZ12	chr5:37838338-37840103	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr5:37839740-37840787	HepG2	liver:	n/a	chr5:37840289-37840299
10	MXI1	chr5:37839252-37840328	IMR90	lung:	n/a	chr5:37839378-37839387
11	POLR2A	chr5:37838942-37839868	U87	brain:	n/a	n/a
12	MAX	chr5:37839785-37840217	MCF-7	breast:	n/a	n/a
13	MAZ	chr5:37838894-37841199	IMR90	lung:	n/a	chr5:37839592-37839602 chr5:37840289-37840299 chr5:37839378-37839388 chr5:37839135-37839145
14	HA-E2F1	chr5:37839600-37840974	MCF-7	breast:	n/a	chr5:37839794-37839804 chr5:37840192-37840201 chr5:37839800-37839810 chr5:37839797-37839807 chr5:37839877-37839887 chr5:37840472-37840482
15	MAX	chr5:37839552-37840816	H1-hESC	embryonic stem cell:	n/a	chr5:37839592-37839602 chr5:37840289-37840299
16	POLR2A	chr5:37838948-37839845	U87	brain:	n/a	n/a
17	POLR2A	chr5:37839787-37840262	H1-neurons	neurons:	n/a	n/a
18	E2F6	chr5:37836391-37840195	H1-hESC	embryonic stem cell:	n/a	chr5:37838340-37838347 chr5:37838955-37838964 chr5:37838113-37838121 chr5:37838400-37838407 chr5:37839794-37839804 chr5:37838739-37838747 chr5:37836831-37836840 chr5:37839800-37839810 chr5:37839797-37839807 chr5:37839877-37839887 chr5:37837060-37837072 chr5:37838340-37838347 chr5:37838739-37838747 chr5:37838112-37838122 chr5:37838663-37838672 chr5:37838113-37838120 chr5:37838340-37838347 chr5:37838113-37838121 chr5:37838112-37838123

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:37839769-37839819	HRE	kidney:	n/a
2	chr5:37839769-37839819	K562	blood:	n/a
3	chr5:37839769-37839819	HNPCEpiC	eye:	n/a
4	chr5:37839769-37839819	SAEC	small airway:	n/a
5	chr5:37839769-37839819	RPTEC	kidney:	n/a
6	chr5:37839769-37839819	Hepatocyte	liver:	n/a
7	chr5:37839769-37839819	GM19239	blood:	n/a
8	chr5:37839769-37839819	ProgFib	skin:	n/a
9	chr5:37839769-37839819	AoSMC	blood vessel:	n/a
10	chr5:37839769-37839819	AG04449	skin:	fetal
11	chr5:37839769-37839819	ECC-1	luminal epithelium:	n/a
12	chr5:37839769-37839819	H1-hESC	embryonic stem cell:	embryo
13	chr5:37839769-37839819	NT2-D1	testis:	n/a
14	chr5:37839769-37839819	BE2_C	brain:	n/a
15	chr5:37839769-37839819	SK-N-SH_RA	brain:	n/a
16	chr5:37839769-37839819	MCF-7	breast:	n/a
17	chr5:37839769-37839819	SK-N-SH	brain:	n/a
18	chr5:37839769-37839819	U87	brain:	n/a
19	chr5:37839769-37839819	Jurkat	blood:	n/a
20	chr5:37839769-37839819	PrEC	prostate:	n/a
21	chr5:37839769-37839819	MCF10A-Er-Src	breast:	n/a
22	chr5:37839769-37839819	HL-60	blood:	n/a
23	chr5:37839769-37839819	NH-A	brain:	n/a
24	chr5:37839769-37839819	HRCEpiC	kidney:	n/a
25	chr5:37839769-37839819	HAEpiC	amniotic membrane:	n/a
26	chr5:37839769-37839819	GM06990	blood:	n/a
27	chr5:37839769-37839819	PFSK-1	brain:	n/a
28	chr5:37839769-37839819	NHDF-neo	bronchial:	n/a
29	chr5:37839769-37839819	GM12891	blood:	n/a
30	chr5:37839769-37839819	AG09309	skin:	n/a
31	chr5:37839769-37839819	HCF	heart:	n/a
32	chr5:37839769-37839819	SKMC	muscle:	n/a
33	chr5:37839769-37839819	HIPEpiC	eye:	n/a
34	chr5:37839769-37839819	LNCaP	prostate:	n/a
35	chr5:37839769-37839819	Hela-S3	cervix:	n/a
36	chr5:37839769-37839819	PANC-1	pancreas:	n/a
37	chr5:37839769-37839819	A549	lung:	n/a
38	chr5:37839769-37839819	HPAEpiC	pulmonary alveolar:	n/a
39	chr5:37839769-37839819	NHBE	bronchial:	n/a
40	chr5:37839769-37839819	Caco-2	colon:	n/a
41	chr5:37839769-37839819	NB4	blood:	n/a
42	chr5:37839769-37839819	AG09319	gingival:	n/a
43	chr5:37839769-37839819	GM12892	blood:	n/a
44	chr5:37839769-37839819	SK-N-MC	brain:	n/a
45	chr5:37839769-37839819	HUVEC	blood vessel:	n/a
46	chr5:37839769-37839819	IMR90	lung:	fetal
47	chr5:37839769-37839819	HMEC	breast:	n/a
48	chr5:37839769-37839819	AG10803	skin:	n/a
49	chr5:37839769-37839819	HCPEpiC	choroid plexus:	n/a
50	chr5:37839769-37839819	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:37834038..37837439-chr5:37839505..37841588,3	MCF-7	breast:

Variant related genes	Relation type
GDNF	TF binding region
GDNF-AS1	TF binding region
GDNF-AS1	CpG island
GDNF	CpG island
ENSG00000168621	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv1844348	chr5:37835398-37840642	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1851519	chr5:37835398-37840642	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3406944	chr5:37838720-37841568	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1833785	chr5:37839618-37840621	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1838210	chr5:37839618-37840621	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv1839230	chr5:37839618-37840621	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1840288	chr5:37839618-37840621	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv597849	chr5:37839618-37840642	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1848849	chr5:37839618-37841045	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1850800	chr5:37839618-37841045	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv13245	chr5:37839636-37840756	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv597850	chr5:37839726-37840243	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv1821997	chr5:37839726-37841045	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv597851	chr5:37839777-37840352	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr5:37834200-37841000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:37834400-37840600	Bivalent Enhancer	Fetal Brain Male	brain
3	chr5:37834400-37841400	Bivalent/Poised TSS	Colonic Mucosa	Colon
4	chr5:37835000-37839800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
5	chr5:37835800-37840000	Bivalent Enhancer	Spleen	Spleen
6	chr5:37836200-37840200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:37836200-37840600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
8	chr5:37836200-37840800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr5:37836200-37840800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr5:37836200-37840800	Active TSS	NHDF-Ad	bronchial
11	chr5:37836200-37841000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr5:37836200-37841000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:37836400-37839800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr5:37836400-37839800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
15	chr5:37836400-37840600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:37836400-37840600	Active TSS	HSMM	muscle
17	chr5:37836400-37840800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr5:37836400-37841200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr5:37836400-37841600	Active TSS	HSMMtube	muscle
20	chr5:37836600-37839800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr5:37836600-37839800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr5:37836600-37840000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
23	chr5:37836600-37840000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
24	chr5:37836600-37840200	Enhancers	Lung	lung
25	chr5:37836600-37841000	Flanking Active TSS	HMEC	breast
26	chr5:37837000-37840600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr5:37837000-37840800	Active TSS	Osteobl	bone
28	chr5:37837800-37839800	Bivalent/Poised TSS	NHLF	lung
29	chr5:37838000-37841200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr5:37838200-37840000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
31	chr5:37838200-37841400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
32	chr5:37838400-37839800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
33	chr5:37838400-37840800	Active TSS	Rectal Smooth Muscle	rectum
34	chr5:37838400-37841000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:37838600-37839800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
36	chr5:37838600-37840200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:37838600-37841000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:37838600-37841000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
39	chr5:37839000-37839800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:37839000-37839800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:37839000-37839800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:37839000-37839800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
43	chr5:37839000-37840000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:37839200-37839800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
45	chr5:37839200-37839800	Flanking Bivalent TSS/Enh	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:37839200-37839800	Bivalent Enhancer	Adipose Nuclei	Adipose
47	chr5:37839200-37839800	Flanking Bivalent TSS/Enh	Fetal Heart	heart
48	chr5:37839200-37839800	Flanking Bivalent TSS/Enh	Placenta	Placenta
49	chr5:37839200-37839800	Enhancers	Gastric	stomach
50	chr5:37839200-37840000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links