Variant report

Variant	rs540432352
Chromosome Location	chr1:239550249-239550250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHRM3-1	chr1:239549865-239550527	NONHSAT010470
2	lnc-CHRM3-1	chr1:239550220-239550527	NONHSAT010472
3	lnc-CHRM3-1	chr1:239550010-239550527	NONHSAT010471
4	lnc-CHRM3-1	chr1:239550010-239550527	NONHSAT139940

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	chr1:239549200-239550400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:239549200-239550400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:239549200-239550400	Active TSS	Brain Cingulate Gyrus	brain
10	chr1:239549200-239550600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr1:239549200-239550600	Active TSS	Brain Anterior Caudate	brain
12	chr1:239549200-239550800	Active TSS	Brain Angular Gyrus	brain
13	chr1:239549200-239550800	Bivalent/Poised TSS	A549	lung
14	chr1:239549200-239551000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
15	chr1:239549200-239551000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:239549200-239551000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
17	chr1:239549200-239551200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr1:239549200-239551200	Active TSS	Brain Substantia Nigra	brain
19	chr1:239549200-239551600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:239549200-239551600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr1:239549200-239551600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr1:239549200-239551800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr1:239549200-239552200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:239549200-239552200	Bivalent/Poised TSS	Fetal Kidney	kidney
25	chr1:239549200-239552200	Active TSS	Pancreas	Pancrea
26	chr1:239549200-239552400	Active TSS	Colon Smooth Muscle	Colon
27	chr1:239549200-239552800	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr1:239549400-239550600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:239549400-239550600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:239549400-239550800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:239549400-239551000	Flanking Active TSS	Liver	Liver
32	chr1:239549400-239551000	Flanking Bivalent TSS/Enh	HMEC	breast
33	chr1:239549400-239551200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:239549400-239551200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:239549400-239551200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:239549400-239551400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:239549400-239551400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
38	chr1:239549400-239551600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
39	chr1:239549400-239551600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:239549400-239551600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
41	chr1:239549400-239551600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr1:239549400-239551600	Active TSS	Gastric	stomach
43	chr1:239549400-239551800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
44	chr1:239549400-239552000	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:239549600-239550400	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:239549600-239550400	Bivalent/Poised TSS	Esophagus	oesophagus
47	chr1:239549600-239550400	Bivalent/Poised TSS	HSMM	muscle
48	chr1:239549600-239550800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:239549600-239550800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:239549600-239550800	Flanking Active TSS	Lung	lung

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