Variant report

Variant	rs578100638
Chromosome Location	chr3:23846939-23846940
allele	A/G
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	BHLHE40	chr3:23846628-23847665	K562	blood:	n/a	chr3:23846798-23846807
2	CTCF	chr3:23846886-23847558	K562	blood:	n/a	chr3:23847105-23847113
3	MTA3	chr3:23846841-23847646	GM12878	blood:	n/a	n/a
4	TBP	chr3:23846849-23847693	K562	blood:	n/a	n/a
5	MAX	chr3:23846867-23847762	A549	lung:	n/a	n/a
6	REST	chr3:23846855-23847961	H1-neurons	neurons:	n/a	chr3:23847879-23847889
7	MYC	chr3:23846891-23846971	NB4	blood:	n/a	n/a
8	RAD21	chr3:23846902-23847297	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZBTB7A	chr3:23846913-23848985	ECC-1	luminal epithelium:	n/a	chr3:23847207-23847216
10	BHLHE40	chr3:23846605-23847174	HepG2	liver:	n/a	chr3:23846798-23846807
11	BHLHE40	chr3:23846641-23847043	A549	lung:	n/a	chr3:23846798-23846807
12	RCOR1	chr3:23846815-23847585	K562	blood:	n/a	n/a
13	HCFC1	chr3:23846781-23847640	K562	blood:	n/a	n/a
14	SIN3A	chr3:23846868-23847867	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAZ	chr3:23846813-23848969	GM12878	blood:	n/a	chr3:23848624-23848633 chr3:23848482-23848492 chr3:23847810-23847820
16	MAZ	chr3:23846771-23849343	K562	blood:	n/a	chr3:23848624-23848633 chr3:23848482-23848492 chr3:23847810-23847820
17	MXI1	chr3:23846611-23849467	SK-N-SH	brain:	n/a	n/a
18	CTCF	chr3:23846820-23846970	GM12873	blood:	n/a	n/a

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:

Variant related genes	Relation type
UBE2E1	TF binding region
ENSG00000197885	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000182247	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000233153	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	esv2446555	chr3:23846940-23846940	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv2221026	chr3:23846940-23846941	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23840000-23847000	Weak transcription	Right Atrium	heart
2	chr3:23846000-23847000	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr3:23846200-23847000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:23846200-23847600	Active TSS	Fetal Brain Male	brain
5	chr3:23846600-23847000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
6	chr3:23846600-23847000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
7	chr3:23846600-23847000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
8	chr3:23846600-23847000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr3:23846600-23847000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:23846600-23847000	Flanking Active TSS	A549	lung
11	chr3:23846600-23847200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:23846600-23847200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:23846600-23847200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr3:23846600-23847600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr3:23846800-23847000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr3:23846800-23847000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
17	chr3:23846800-23847000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:23846800-23847000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:23846800-23847000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr3:23846800-23847000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:23846800-23847000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr3:23846800-23847000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:23846800-23847000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr3:23846800-23847000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:23846800-23847000	Enhancers	Brain Substantia Nigra	brain
26	chr3:23846800-23847000	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr3:23846800-23847000	Active TSS	Fetal Heart	heart
28	chr3:23846800-23847000	Flanking Active TSS	Fetal Kidney	kidney
29	chr3:23846800-23847000	Enhancers	Fetal Lung	lung
30	chr3:23846800-23847000	Enhancers	Fetal Thymus	thymus
31	chr3:23846800-23847000	Flanking Active TSS	HepG2	liver
32	chr3:23846800-23847000	Flanking Active TSS	HSMM	muscle
33	chr3:23846800-23847000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
34	chr3:23846800-23847000	Flanking Active TSS	NHEK	skin
35	chr3:23846800-23847200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:23846800-23847200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:23846800-23847200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:23846800-23847200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr3:23846800-23847200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr3:23846800-23847200	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr3:23846800-23847200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr3:23846800-23847200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr3:23846800-23847200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr3:23846800-23847200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr3:23846800-23847200	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr3:23846800-23847200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:23846800-23847200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr3:23846800-23847200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:23846800-23847200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:23846800-23847200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links