Variant report

Variant	rs13161180
Chromosome Location	chr5:59189705-59189706
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	RAD21	chr5:59189341-59190176	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr5:59189560-59189710	HCFaa	heart:	n/a	n/a
3	REST	chr5:59189686-59190039	GM12878	blood:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189914-59189924
4	MAX	chr5:59189681-59190201	MCF-7	breast:	n/a	n/a
5	REST	chr5:59189653-59190151	U87	brain:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189914-59189924
6	SIN3A	chr5:59187759-59190451	H1-hESC	embryonic stem cell:	n/a	chr5:59187953-59187961 chr5:59189914-59189923 chr5:59187954-59187967
7	CHD1	chr5:59189704-59189990	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr5:59189683-59190124	Hela-S3	cervix:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189914-59189924
9	REST	chr5:59189349-59190286	U87	brain:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189560-59189573 chr5:59189914-59189924
10	SIN3AK20	chr5:59189522-59190328	MCF-7	breast:	n/a	n/a
11	REST	chr5:59189690-59190197	Hela-S3	cervix:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189914-59189924
12	TBP	chr5:59189389-59190169	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3AK20	chr5:59189657-59190106	SK-N-SH	brain:	n/a	n/a
14	RAD21	chr5:59189277-59190023	SK-N-SH_RA	brain:	n/a	n/a
15	SIN3AK20	chr5:59189607-59190107	H1-hESC	embryonic stem cell:	n/a	n/a
16	REST	chr5:59189222-59190519	SK-N-SH	brain:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189560-59189573 chr5:59189914-59189924
17	REST	chr5:59189333-59190444	H1-neurons	neurons:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189560-59189573 chr5:59189914-59189924
18	ZNF143	chr5:59189627-59190374	H1-hESC	embryonic stem cell:	n/a	n/a
19	REST	chr5:59189278-59190284	ECC-1	luminal epithelium:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189560-59189573 chr5:59189914-59189924
20	CTCF	chr5:59189640-59189790	HBMEC	blood vessel:	n/a	n/a
21	REST	chr5:59189307-59190140	SK-N-SH	brain:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189560-59189573 chr5:59189914-59189924
22	HDAC2	chr5:59189598-59190152	MCF-7	breast:	n/a	n/a
23	CTCF	chr5:59189600-59189750	HCPEpiC	choroid plexus:	n/a	n/a
24	REST	chr5:59189534-59190427	A549	lung:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189560-59189573 chr5:59189914-59189924
25	REST	chr5:59189227-59190214	PFSK-1	brain:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189560-59189573 chr5:59189914-59189924
26	RAD21	chr5:59189539-59190048	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr5:59189580-59189730	HEK293	kidney:	n/a	n/a
28	RAD21	chr5:59189369-59189718	SK-N-SH_RA	brain:	n/a	n/a
29	REST	chr5:59189635-59190335	PANC-1	pancreas:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189914-59189924
30	REST	chr5:59189256-59190168	U87	brain:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189560-59189573 chr5:59189914-59189924
31	GATA3	chr5:59189660-59190117	T-47D	breast:	n/a	n/a
32	REST	chr5:59189614-59190215	HL-60	blood:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189914-59189924
33	CTCF	chr5:59189680-59189830	HCM	heart:	n/a	n/a
34	CTBP2	chr5:59189311-59190165	H1-hESC	embryonic stem cell:	n/a	n/a
35	REST	chr5:59189385-59190263	H1-hESC	embryonic stem cell:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189560-59189573 chr5:59189914-59189924
36	GATA2	chr5:59189566-59190525	SH-SY5Y	brain:	n/a	chr5:59190163-59190173 chr5:59190158-59190174 chr5:59190163-59190170 chr5:59190156-59190177 chr5:59190161-59190171 chr5:59190161-59190170
37	CTCF	chr5:59189600-59189890	HPAF	blood vessel:	n/a	n/a
38	MAX	chr5:59189678-59190152	SK-N-SH	brain:	n/a	n/a
39	MAX	chr5:59189683-59190208	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr5:59189580-59189730	WERI-Rb-1	eye:	n/a	n/a
41	GATA3	chr5:59189616-59190188	MCF-7	breast:	n/a	chr5:59190163-59190173 chr5:59190158-59190174 chr5:59190163-59190170 chr5:59190156-59190177 chr5:59190161-59190171 chr5:59190161-59190170
42	ZNF263	chr5:59189598-59190289	HEK293-T-REx	kidney:	n/a	chr5:59189757-59189766
43	POLR2A	chr5:59187392-59190596	H1-neurons	neurons:	n/a	n/a
44	REST	chr5:59189651-59190300	A549	lung:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189914-59189924
45	REST	chr5:59189679-59190217	PFSK-1	brain:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189914-59189924
46	MAX	chr5:59189665-59190174	ECC-1	luminal epithelium:	n/a	n/a
47	YY1	chr5:59189647-59190057	H1-hESC	embryonic stem cell:	n/a	chr5:59189844-59189853
48	MXI1	chr5:59189580-59190294	IMR90	lung:	n/a	n/a
49	REST	chr5:59189567-59190245	GM12878	blood:	n/a	chr5:59189824-59189842 chr5:59189911-59189920 chr5:59189914-59189924
50	POLR2A	chr5:59189261-59190303	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13162650	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162864	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175909	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546364	1.00[ASN][1000 genomes]
rs34918713	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59807464	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879288	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7710463	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717043	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59186600-59190600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr5:59187400-59190200	Active TSS	HSMMtube	muscle
3	chr5:59187800-59190000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr5:59187800-59190200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr5:59187800-59190200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:59187800-59190400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr5:59187800-59190600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr5:59187800-59190600	Active TSS	Brain Anterior Caudate	brain
9	chr5:59188000-59190000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr5:59188000-59190200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
11	chr5:59188000-59190400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr5:59188200-59190200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr5:59188200-59190200	Enhancers	Spleen	Spleen
14	chr5:59188600-59190200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:59188600-59190200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
16	chr5:59188800-59189800	Flanking Active TSS	Gastric	stomach
17	chr5:59188800-59190000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:59188800-59190000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
19	chr5:59188800-59190000	Active TSS	HSMM	muscle
20	chr5:59188800-59190200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:59188800-59190200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr5:59188800-59190200	Bivalent Enhancer	Ovary	ovary
23	chr5:59188800-59190600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr5:59189000-59189800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:59189000-59189800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:59189000-59189800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:59189000-59189800	Active TSS	Aorta	Aorta
28	chr5:59189000-59189800	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr5:59189000-59190000	Active TSS	Muscle Satellite Cultured Cells	--
30	chr5:59189000-59190000	Active TSS	Brain Angular Gyrus	brain
31	chr5:59189000-59190000	Active TSS	Brain Substantia Nigra	brain
32	chr5:59189000-59190200	ZNF genes & repeats	Lung	lung
33	chr5:59189000-59190600	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr5:59189000-59190600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:59189000-59190800	Active TSS	Fetal Brain Female	brain
36	chr5:59189200-59190000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:59189200-59190000	Active TSS	Brain Cingulate Gyrus	brain
38	chr5:59189200-59190400	Active TSS	H9 Cell Line	embryonic stem cell
39	chr5:59189200-59190400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
40	chr5:59189400-59189800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:59189400-59189800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:59189400-59189800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:59189400-59189800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr5:59189400-59189800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:59189400-59189800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
46	chr5:59189400-59189800	Bivalent Enhancer	Psoas Muscle	Psoas
47	chr5:59189400-59189800	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr5:59189400-59189800	Flanking Active TSS	Right Atrium	heart
49	chr5:59189400-59189800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
50	chr5:59189400-59190000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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