Variant report

Variant	rs186888898
Chromosome Location	chr1:239549987-239549988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:93)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:93 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:239549880-239550030	SAEC	small airway:	n/a	n/a
2	POLR2A	chr1:239549678-239549988	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr1:239549860-239550010	HRPEpiC	eye:	n/a	n/a
4	CTCF	chr1:239549860-239550010	HEK293	kidney:	n/a	n/a
5	MAX	chr1:239549439-239550219	A549	lung:	n/a	chr1:239549743-239549753
6	CTCF	chr1:239549900-239550050	Caco-2	colon:	n/a	n/a
7	MYC	chr1:239549545-239550317	MCF10A-Er-Src	breast:	n/a	chr1:239549743-239549753
8	POLR2A	chr1:239549628-239550119	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr1:239549556-239550589	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr1:239549269-239551373	H1-hESC	embryonic stem cell:	n/a	chr1:239551280-239551289
11	POLR2A	chr1:239549785-239550031	ECC-1	luminal epithelium:	n/a	n/a
12	CTCF	chr1:239549875-239550016	SK-N-SH_RA	brain:	n/a	n/a
13	MXI1	chr1:239549089-239552581	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr1:239549880-239550030	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr1:239549900-239550050	HAc	cerebellar:	n/a	n/a
16	E2F4	chr1:239549204-239550159	MCF10A-Er-Src	breast:	n/a	n/a
17	CTCF	chr1:239549920-239550070	BJ	skin:	n/a	n/a
18	CTCF	chr1:239549880-239550030	HMEC	breast:	n/a	n/a
19	CTCF	chr1:239549926-239550035	LNCaP	prostate:	n/a	n/a
20	CTCF	chr1:239549900-239550050	BJ	skin:	n/a	n/a
21	CTCF	chr1:239549870-239550030	SK-N-SH_RA	brain:	n/a	n/a
22	POLR2A	chr1:239549565-239550094	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr1:239549678-239550002	Gliobla	brain:	n/a	n/a
24	EGR1	chr1:239549954-239550354	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr1:239549833-239550091	Pancreas_OC	pancreas:	n/a	n/a
26	CTCF	chr1:239549900-239550050	HEEpiC	esophagus:	n/a	n/a
27	TBP	chr1:239549636-239550416	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr1:239549880-239550030	HRPEpiC	eye:	n/a	n/a
29	E2F6	chr1:239549587-239550013	A549	lung:	n/a	n/a
30	MAX	chr1:239549391-239551252	H1-hESC	embryonic stem cell:	n/a	chr1:239549743-239549753
31	RAD21	chr1:239549587-239550110	SK-N-SH_RA	brain:	n/a	n/a
32	TEAD4	chr1:239549646-239550070	H1-hESC	embryonic stem cell:	n/a	n/a
33	KAP1	chr1:239548992-239551772	HEK293	kidney:	n/a	n/a
34	MAX	chr1:239549542-239551431	H1-hESC	embryonic stem cell:	n/a	chr1:239549743-239549753
35	GTF2F1	chr1:239549750-239550316	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr1:239549900-239550050	BE2_C	brain:	n/a	n/a
37	CTCF	chr1:239549911-239550003	MCF-7	breast:	n/a	n/a
38	TEAD4	chr1:239549554-239550016	H1-hESC	embryonic stem cell:	n/a	n/a
39	MXI1	chr1:239549646-239550053	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr1:239549894-239550055	GM19238	blood:	n/a	n/a
41	CTCF	chr1:239549860-239550010	Caco-2	colon:	n/a	n/a
42	RAD21	chr1:239549732-239550178	A549	lung:	n/a	n/a
43	CTCF	chr1:239549900-239550050	AG09309	skin:	n/a	n/a
44	CHD2	chr1:239549614-239550093	H1-hESC	embryonic stem cell:	n/a	chr1:239549736-239549746
45	SUZ12	chr1:239549649-239552103	NT2-D1	testis:	n/a	n/a
46	SIN3A	chr1:239549304-239551123	H1-hESC	embryonic stem cell:	n/a	chr1:239550548-239550557
47	CTCF	chr1:239549860-239550010	SK-N-SH_RA	brain:	n/a	n/a
48	MAX	chr1:239549637-239549990	SK-N-SH	brain:	n/a	chr1:239549743-239549753
49	MAX	chr1:239549472-239550615	ECC-1	luminal epithelium:	n/a	chr1:239549743-239549753
50	CTCF	chr1:239549900-239550050	RPTEC	kidney:	n/a	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHRM3-1	chr1:239549865-239550527	NONHSAT010470

No data

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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239548800-239550800	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:239548800-239552400	Active TSS	Ovary	ovary
3	chr1:239548800-239553200	Active TSS	Stomach Smooth Muscle	stomach
4	chr1:239549000-239550400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:239549000-239550600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr1:239549000-239551600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:239549200-239550000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr1:239549200-239550000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
9	chr1:239549200-239550400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:239549200-239550400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:239549200-239550400	Active TSS	Brain Cingulate Gyrus	brain
12	chr1:239549200-239550600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:239549200-239550600	Active TSS	Brain Anterior Caudate	brain
14	chr1:239549200-239550800	Active TSS	Brain Angular Gyrus	brain
15	chr1:239549200-239550800	Bivalent/Poised TSS	A549	lung
16	chr1:239549200-239551000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr1:239549200-239551000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:239549200-239551000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
19	chr1:239549200-239551200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr1:239549200-239551200	Active TSS	Brain Substantia Nigra	brain
21	chr1:239549200-239551600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:239549200-239551600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:239549200-239551600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr1:239549200-239551800	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr1:239549200-239552200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:239549200-239552200	Bivalent/Poised TSS	Fetal Kidney	kidney
27	chr1:239549200-239552200	Active TSS	Pancreas	Pancrea
28	chr1:239549200-239552400	Active TSS	Colon Smooth Muscle	Colon
29	chr1:239549200-239552800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr1:239549400-239550000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
31	chr1:239549400-239550200	Active TSS	Right Atrium	heart
32	chr1:239549400-239550600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:239549400-239550600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:239549400-239550800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:239549400-239551000	Flanking Active TSS	Liver	Liver
36	chr1:239549400-239551000	Flanking Bivalent TSS/Enh	HMEC	breast
37	chr1:239549400-239551200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:239549400-239551200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:239549400-239551200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:239549400-239551400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:239549400-239551400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
42	chr1:239549400-239551600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:239549400-239551600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:239549400-239551600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
45	chr1:239549400-239551600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr1:239549400-239551600	Active TSS	Gastric	stomach
47	chr1:239549400-239551800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
48	chr1:239549400-239552000	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr1:239549600-239550000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:239549600-239550000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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