Variant report

Variant	rs528331365
Chromosome Location	chr1:239549655-239549656
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

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	POLR2A	chr1:239549628-239550119	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr1:239549556-239550589	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr1:239549269-239551373	H1-hESC	embryonic stem cell:	n/a	chr1:239551280-239551289
6	MXI1	chr1:239549089-239552581	SK-N-SH	brain:	n/a	n/a
7	E2F4	chr1:239549204-239550159	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:239549565-239550094	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBP	chr1:239549636-239550416	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr1:239549587-239550013	A549	lung:	n/a	n/a
11	MAX	chr1:239549391-239551252	H1-hESC	embryonic stem cell:	n/a	chr1:239549743-239549753
12	RAD21	chr1:239549587-239550110	SK-N-SH_RA	brain:	n/a	n/a
13	TEAD4	chr1:239549646-239550070	H1-hESC	embryonic stem cell:	n/a	n/a
14	KAP1	chr1:239548992-239551772	HEK293	kidney:	n/a	n/a
15	MAX	chr1:239549542-239551431	H1-hESC	embryonic stem cell:	n/a	chr1:239549743-239549753
16	TEAD4	chr1:239549554-239550016	H1-hESC	embryonic stem cell:	n/a	n/a
17	MXI1	chr1:239549646-239550053	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:239549564-239549931	MCF10A-Er-Src	breast:	n/a	n/a
19	CHD2	chr1:239549614-239550093	H1-hESC	embryonic stem cell:	n/a	chr1:239549736-239549746
20	SUZ12	chr1:239549649-239552103	NT2-D1	testis:	n/a	n/a
21	MYC	chr1:239549351-239549885	H1-hESC	embryonic stem cell:	n/a	chr1:239549743-239549753
22	SIN3A	chr1:239549304-239551123	H1-hESC	embryonic stem cell:	n/a	chr1:239550548-239550557
23	MAX	chr1:239549637-239549990	SK-N-SH	brain:	n/a	chr1:239549743-239549753
24	MAX	chr1:239549472-239550615	ECC-1	luminal epithelium:	n/a	chr1:239549743-239549753
25	ZNF263	chr1:239549320-239551659	HEK293-T-REx	kidney:	n/a	chr1:239549888-239549909 chr1:239549912-239549933
26	USF2	chr1:239549611-239550270	H1-hESC	embryonic stem cell:	n/a	n/a
27	TCF7L2	chr1:239549266-239549990	PANC-1	pancreas:	n/a	n/a
28	YY1	chr1:239549471-239550008	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr1:239549653-239550100	H1-hESC	embryonic stem cell:	n/a	n/a
30	ZNF143	chr1:239549497-239550377	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr1:239549524-239550046	A549	lung:	n/a	chr1:239549743-239549753
32	RAD21	chr1:239549636-239550065	SK-N-SH_RA	brain:	n/a	n/a
33	E2F6	chr1:239549434-239550039	A549	lung:	n/a	n/a
34	REST	chr1:239549613-239550049	SK-N-SH	brain:	n/a	n/a
35	CTBP2	chr1:239549362-239551324	H1-hESC	embryonic stem cell:	n/a	n/a
36	TCF7L2	chr1:239549213-239549937	HEK293	kidney:	n/a	n/a
37	RAD21	chr1:239549574-239550474	H1-hESC	embryonic stem cell:	n/a	n/a
38	MYC	chr1:239549333-239550066	MCF10A-Er-Src	breast:	n/a	chr1:239549743-239549753
39	TCF7L2	chr1:239549221-239549795	Hela-S3	cervix:	n/a	n/a
40	MAX	chr1:239549431-239550200	H1-hESC	embryonic stem cell:	n/a	chr1:239549743-239549753
41	RAD21	chr1:239549141-239550476	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr1:239549584-239550067	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr1:239549651-239550114	H1-neurons	neurons:	n/a	n/a
44	MAX	chr1:239549484-239550462	ECC-1	luminal epithelium:	n/a	chr1:239549743-239549753

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:239549626-239549676	NHBE	bronchial:	n/a
2	chr1:239549626-239549676	HNPCEpiC	eye:	n/a
3	chr1:239549626-239549676	HL-60	blood:	n/a
4	chr1:239549626-239549676	HCM	heart:	n/a
5	chr1:239549626-239549676	RPTEC	kidney:	n/a
6	chr1:239549626-239549676	HepG2	liver:	n/a
7	chr1:239549626-239549676	CMK	blood:	n/a
8	chr1:239549626-239549676	H1-hESC	embryonic stem cell:	embryo
9	chr1:239549626-239549676	HRE	kidney:	n/a
10	chr1:239549626-239549676	HUVEC	blood vessel:	n/a
11	chr1:239549626-239549676	SKMC	muscle:	n/a
12	chr1:239549626-239549676	K562	blood:	n/a
13	chr1:239549626-239549676	SK-N-SH_RA	brain:	n/a
14	chr1:239549626-239549676	ProgFib	skin:	n/a
15	chr1:239549626-239549676	GM12878	blood:	n/a
16	chr1:239549626-239549676	SAEC	small airway:	n/a
17	chr1:239549626-239549676	T-47D	breast:	n/a
18	chr1:239549626-239549676	Caco-2	colon:	n/a
19	chr1:239549626-239549676	U87	brain:	n/a
20	chr1:239549626-239549676	HCT-116	colon:	n/a
21	chr1:239549626-239549676	AG09309	skin:	n/a
22	chr1:239549626-239549676	HRPEpiC	eye:	n/a
23	chr1:239549626-239549676	PrEC	prostate:	n/a
24	chr1:239549626-239549676	HIPEpiC	eye:	n/a
25	chr1:239549626-239549676	HEEpiC	esophagus:	n/a
26	chr1:239549626-239549676	MCF-7	breast:	n/a
27	chr1:239549626-239549676	HEK293	kidney:	embryo
28	chr1:239549626-239549676	SK-N-MC	brain:	n/a
29	chr1:239549626-239549676	NHDF-neo	bronchial:	n/a
30	chr1:239549626-239549676	MCF10A-Er-Src	breast:	n/a
31	chr1:239549626-239549676	GM12892	blood:	n/a
32	chr1:239549626-239549676	IMR90	lung:	fetal
33	chr1:239549626-239549676	PFSK-1	brain:	n/a
34	chr1:239549626-239549676	HCPEpiC	choroid plexus:	n/a
35	chr1:239549626-239549676	NH-A	brain:	n/a
36	chr1:239549626-239549676	BJ	skin:	n/a
37	chr1:239549626-239549676	GM06990	blood:	n/a
38	chr1:239549626-239549676	NT2-D1	testis:	n/a
39	chr1:239549626-239549676	ECC-1	luminal epithelium:	n/a
40	chr1:239549626-239549676	A549	lung:	n/a
41	chr1:239549626-239549676	Jurkat	blood:	n/a
42	chr1:239549626-239549676	GM12891	blood:	n/a
43	chr1:239549626-239549676	AG04450	lung:	fetal
44	chr1:239549626-239549676	HCF	heart:	n/a
45	chr1:239549626-239549676	AG10803	skin:	n/a
46	chr1:239549626-239549676	LNCaP	prostate:	n/a
47	chr1:239549626-239549676	BE2_C	brain:	n/a
48	chr1:239549626-239549676	NB4	blood:	n/a
49	chr1:239549626-239549676	GM19239	blood:	n/a
50	chr1:239549626-239549676	Hela-S3	cervix:	n/a

No data

Variant related genes	Relation type
CHRM3	TF binding region
CHRM3	CpG island

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:103 , 50 per page) page: 1 2 3

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	chr1:239549000-239550400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:239549000-239550600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr1:239549000-239551600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:239549200-239549800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr1:239549200-239549800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:239549200-239549800	Flanking Bivalent TSS/Enh	Fetal Heart	heart
11	chr1:239549200-239549800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
12	chr1:239549200-239549800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr1:239549200-239550000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr1:239549200-239550000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
15	chr1:239549200-239550400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:239549200-239550400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:239549200-239550400	Active TSS	Brain Cingulate Gyrus	brain
18	chr1:239549200-239550600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:239549200-239550600	Active TSS	Brain Anterior Caudate	brain
20	chr1:239549200-239550800	Active TSS	Brain Angular Gyrus	brain
21	chr1:239549200-239550800	Bivalent/Poised TSS	A549	lung
22	chr1:239549200-239551000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr1:239549200-239551000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:239549200-239551000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
25	chr1:239549200-239551200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr1:239549200-239551200	Active TSS	Brain Substantia Nigra	brain
27	chr1:239549200-239551600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:239549200-239551600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr1:239549200-239551600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr1:239549200-239551800	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr1:239549200-239552200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr1:239549200-239552200	Bivalent/Poised TSS	Fetal Kidney	kidney
33	chr1:239549200-239552200	Active TSS	Pancreas	Pancrea
34	chr1:239549200-239552400	Active TSS	Colon Smooth Muscle	Colon
35	chr1:239549200-239552800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr1:239549400-239549800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
37	chr1:239549400-239549800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
38	chr1:239549400-239549800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
39	chr1:239549400-239549800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
40	chr1:239549400-239549800	Flanking Bivalent TSS/Enh	NH-A	brain
41	chr1:239549400-239550000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
42	chr1:239549400-239550200	Active TSS	Right Atrium	heart
43	chr1:239549400-239550600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:239549400-239550600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:239549400-239550800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:239549400-239551000	Flanking Active TSS	Liver	Liver
47	chr1:239549400-239551000	Flanking Bivalent TSS/Enh	HMEC	breast
48	chr1:239549400-239551200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:239549400-239551200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:239549400-239551200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

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