Variant report

Variant	rs563582450
Chromosome Location	chr1:239549547-239549548
allele	A/C
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	MAX	chr1:239549439-239550219	A549	lung:	n/a	chr1:239549743-239549753
2	MYC	chr1:239549545-239550317	MCF10A-Er-Src	breast:	n/a	chr1:239549743-239549753
3	E2F6	chr1:239549269-239551373	H1-hESC	embryonic stem cell:	n/a	chr1:239551280-239551289
4	MXI1	chr1:239549089-239552581	SK-N-SH	brain:	n/a	n/a
5	E2F4	chr1:239549204-239550159	MCF10A-Er-Src	breast:	n/a	n/a
6	MAX	chr1:239549391-239551252	H1-hESC	embryonic stem cell:	n/a	chr1:239549743-239549753
7	KAP1	chr1:239548992-239551772	HEK293	kidney:	n/a	n/a
8	MAX	chr1:239549542-239551431	H1-hESC	embryonic stem cell:	n/a	chr1:239549743-239549753
9	MYC	chr1:239549351-239549885	H1-hESC	embryonic stem cell:	n/a	chr1:239549743-239549753
10	SIN3A	chr1:239549304-239551123	H1-hESC	embryonic stem cell:	n/a	chr1:239550548-239550557
11	MAX	chr1:239549472-239550615	ECC-1	luminal epithelium:	n/a	chr1:239549743-239549753
12	ZNF263	chr1:239549320-239551659	HEK293-T-REx	kidney:	n/a	chr1:239549888-239549909 chr1:239549912-239549933
13	TCF7L2	chr1:239549266-239549990	PANC-1	pancreas:	n/a	n/a
14	YY1	chr1:239549471-239550008	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZNF143	chr1:239549497-239550377	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr1:239549524-239550046	A549	lung:	n/a	chr1:239549743-239549753
17	E2F6	chr1:239549434-239550039	A549	lung:	n/a	n/a
18	CTBP2	chr1:239549362-239551324	H1-hESC	embryonic stem cell:	n/a	n/a
19	TCF7L2	chr1:239549213-239549937	HEK293	kidney:	n/a	n/a
20	MYC	chr1:239549333-239550066	MCF10A-Er-Src	breast:	n/a	chr1:239549743-239549753
21	TCF7L2	chr1:239549221-239549795	Hela-S3	cervix:	n/a	n/a
22	MAX	chr1:239549431-239550200	H1-hESC	embryonic stem cell:	n/a	chr1:239549743-239549753
23	RAD21	chr1:239549141-239550476	SK-N-SH	brain:	n/a	n/a
24	MAX	chr1:239549484-239550462	ECC-1	luminal epithelium:	n/a	chr1:239549743-239549753

Variant related genes	Relation type
CHRM3	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1006640	chr1:239290853-239658788	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535358	chr1:239290853-239658788	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv468617	chr1:239350728-239564682	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv549434	chr1:239350728-239564682	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1002418	chr1:239355675-239552376	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1001152	chr1:239355675-239564682	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1013763	chr1:239356155-239564682	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv869803	chr1:239360129-239566743	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1006706	chr1:239367862-239551655	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv535359	chr1:239367862-239551655	Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv873349	chr1:239475925-239587512	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3373454	chr1:239495349-239670615	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv873350	chr1:239498915-239648140	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv833037	chr1:239522168-239699412	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv3356808	chr1:239549154-239551702	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239548800-239549800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:239548800-239550800	Active TSS	Rectal Smooth Muscle	rectum
3	chr1:239548800-239552400	Active TSS	Ovary	ovary
4	chr1:239548800-239553200	Active TSS	Stomach Smooth Muscle	stomach
5	chr1:239549000-239549600	Bivalent Enhancer	Stomach Mucosa	stomach
6	chr1:239549000-239550400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:239549000-239550600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:239549000-239551600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:239549200-239549600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:239549200-239549600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr1:239549200-239549600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
12	chr1:239549200-239549600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
13	chr1:239549200-239549600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
14	chr1:239549200-239549600	Active TSS	Duodenum Mucosa	Duodenum
15	chr1:239549200-239549600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
16	chr1:239549200-239549600	Bivalent/Poised TSS	Right Ventricle	heart
17	chr1:239549200-239549800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr1:239549200-239549800	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr1:239549200-239549800	Flanking Bivalent TSS/Enh	Fetal Heart	heart
20	chr1:239549200-239549800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
21	chr1:239549200-239549800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr1:239549200-239550000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr1:239549200-239550000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
24	chr1:239549200-239550400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:239549200-239550400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:239549200-239550400	Active TSS	Brain Cingulate Gyrus	brain
27	chr1:239549200-239550600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:239549200-239550600	Active TSS	Brain Anterior Caudate	brain
29	chr1:239549200-239550800	Active TSS	Brain Angular Gyrus	brain
30	chr1:239549200-239550800	Bivalent/Poised TSS	A549	lung
31	chr1:239549200-239551000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
32	chr1:239549200-239551000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:239549200-239551000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
34	chr1:239549200-239551200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
35	chr1:239549200-239551200	Active TSS	Brain Substantia Nigra	brain
36	chr1:239549200-239551600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:239549200-239551600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
38	chr1:239549200-239551600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr1:239549200-239551800	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr1:239549200-239552200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:239549200-239552200	Bivalent/Poised TSS	Fetal Kidney	kidney
42	chr1:239549200-239552200	Active TSS	Pancreas	Pancrea
43	chr1:239549200-239552400	Active TSS	Colon Smooth Muscle	Colon
44	chr1:239549200-239552800	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr1:239549400-239549600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
46	chr1:239549400-239549600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:239549400-239549600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:239549400-239549600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
49	chr1:239549400-239549600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
50	chr1:239549400-239549600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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