Variant report

Variant	rs554706663
Chromosome Location	chr3:23846692-23846693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr3:23846628-23847665	K562	blood:	n/a	chr3:23846798-23846807
2	BHLHE40	chr3:23846605-23847174	HepG2	liver:	n/a	chr3:23846798-23846807
3	BHLHE40	chr3:23846641-23847043	A549	lung:	n/a	chr3:23846798-23846807
4	MXI1	chr3:23846611-23849467	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:23846692-23846742	NT2-D1	testis:	n/a
2	chr3:23846692-23846742	HCT-116	colon:	n/a
3	chr3:23846692-23846742	T-47D	breast:	n/a
4	chr3:23846692-23846742	A549	lung:	n/a
5	chr3:23846692-23846742	CMK	blood:	n/a
6	chr3:23846692-23846742	ProgFib	skin:	n/a
7	chr3:23846692-23846742	NH-A	brain:	n/a
8	chr3:23846692-23846742	SKMC	muscle:	n/a
9	chr3:23846692-23846742	U87	brain:	n/a
10	chr3:23846692-23846742	HepG2	liver:	n/a
11	chr3:23846692-23846742	GM12878	blood:	n/a
12	chr3:23846692-23846742	HIPEpiC	eye:	n/a
13	chr3:23846692-23846742	SK-N-SH_RA	brain:	n/a
14	chr3:23846692-23846742	HAEpiC	amniotic membrane:	n/a
15	chr3:23846692-23846742	PANC-1	pancreas:	n/a
16	chr3:23846692-23846742	Hela-S3	cervix:	n/a
17	chr3:23846692-23846742	HPAEpiC	pulmonary alveolar:	n/a
18	chr3:23846692-23846742	GM19239	blood:	n/a
19	chr3:23846692-23846742	AG04449	skin:	fetal
20	chr3:23846692-23846742	AG09319	gingival:	n/a
21	chr3:23846692-23846742	MCF10A-Er-Src	breast:	n/a
22	chr3:23846692-23846742	Caco-2	colon:	n/a
23	chr3:23846692-23846742	SK-N-MC	brain:	n/a
24	chr3:23846692-23846742	GM12892	blood:	n/a
25	chr3:23846692-23846742	PrEC	prostate:	n/a
26	chr3:23846692-23846742	BJ	skin:	n/a
27	chr3:23846692-23846742	NHDF-neo	bronchial:	n/a
28	chr3:23846692-23846742	AoSMC	blood vessel:	n/a
29	chr3:23846692-23846742	HRE	kidney:	n/a
30	chr3:23846692-23846742	Hepatocyte	liver:	n/a
31	chr3:23846692-23846742	HL-60	blood:	n/a
32	chr3:23846692-23846742	IMR90	lung:	fetal
33	chr3:23846692-23846742	AG10803	skin:	n/a
34	chr3:23846692-23846742	LNCaP	prostate:	n/a
35	chr3:23846692-23846742	Jurkat	blood:	n/a
36	chr3:23846692-23846742	SAEC	small airway:	n/a
37	chr3:23846692-23846742	HEEpiC	esophagus:	n/a
38	chr3:23846692-23846742	BE2_C	brain:	n/a
39	chr3:23846692-23846742	HCPEpiC	choroid plexus:	n/a
40	chr3:23846692-23846742	K562	blood:	n/a
41	chr3:23846692-23846742	HMEC	breast:	n/a
42	chr3:23846692-23846742	GM06990	blood:	n/a
43	chr3:23846692-23846742	AG09309	skin:	n/a
44	chr3:23846692-23846742	MCF-7	breast:	n/a
45	chr3:23846692-23846742	AG04450	lung:	fetal
46	chr3:23846692-23846742	RPTEC	kidney:	n/a
47	chr3:23846692-23846742	ECC-1	luminal epithelium:	n/a
48	chr3:23846692-23846742	NB4	blood:	n/a
49	chr3:23846692-23846742	GM12891	blood:	n/a
50	chr3:23846692-23846742	HNPCEpiC	eye:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:23846193..23848940-chr3:24535065..24537255,2	K562	blood:
2	chr3:23846380..23850116-chr3:23956700..23960461,6	MCF-7	breast:
3	chr3:23243031..23244851-chr3:23845499..23848237,2	MCF-7	breast:
4	chr3:23846531..23848270-chr3:23987055..23988984,2	MCF-7	breast:
5	chr3:23845112..23848622-chr3:23958029..23961906,4	K562	blood:
6	chr3:23845393..23848355-chr3:23958587..23960710,4	K562	blood:

No data

Variant related genes	Relation type
UBE2E1	TF binding region
UBE2E1	CpG island
ENSG00000174738	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000182247	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000233153	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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834637	chr3:23703928-23886144	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3378886	chr3:23846373-23849821	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23840000-23847000	Weak transcription	Right Atrium	heart
2	chr3:23840200-23846800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:23840200-23846800	Weak transcription	GM12878-XiMat	blood
4	chr3:23843800-23846800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:23844400-23846800	Enhancers	Fetal Intestine Small	intestine
6	chr3:23844400-23846800	Weak transcription	Small Intestine	intestine
7	chr3:23845600-23846800	Weak transcription	Fetal Lung	lung
8	chr3:23846000-23846800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:23846000-23846800	Enhancers	Primary hematopoietic stem cells	blood
10	chr3:23846000-23846800	Enhancers	Fetal Intestine Large	intestine
11	chr3:23846000-23846800	Enhancers	K562	blood
12	chr3:23846000-23847000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr3:23846200-23846800	Enhancers	Fetal Kidney	kidney
14	chr3:23846200-23847000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:23846200-23847600	Active TSS	Fetal Brain Male	brain
16	chr3:23846400-23846800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:23846400-23846800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:23846400-23846800	Enhancers	Duodenum Mucosa	Duodenum
19	chr3:23846600-23846800	Active TSS	H1 Cell Line	embryonic stem cell
20	chr3:23846600-23846800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
21	chr3:23846600-23846800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:23846600-23846800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:23846600-23846800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:23846600-23846800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr3:23846600-23846800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:23846600-23846800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:23846600-23846800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:23846600-23846800	Enhancers	Primary B cells from cord blood	blood
29	chr3:23846600-23846800	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:23846600-23846800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:23846600-23846800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr3:23846600-23846800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:23846600-23846800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:23846600-23846800	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr3:23846600-23846800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:23846600-23846800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:23846600-23846800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr3:23846600-23846800	Enhancers	Fetal Brain Female	brain
39	chr3:23846600-23846800	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr3:23846600-23846800	Enhancers	Hela-S3	cervix
41	chr3:23846600-23846800	Bivalent Enhancer	HepG2	liver
42	chr3:23846600-23846800	Enhancers	HMEC	breast
43	chr3:23846600-23847000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
44	chr3:23846600-23847000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
45	chr3:23846600-23847000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
46	chr3:23846600-23847000	Enhancers	Primary T cells fromperipheralblood	blood
47	chr3:23846600-23847000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:23846600-23847000	Flanking Active TSS	A549	lung
49	chr3:23846600-23847200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:23846600-23847200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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