Variant report

Variant	rs1992236
Chromosome Location	chr15:55881111-55881112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:244)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:55879713-55881300	ECC-1	luminal epithelium:	n/a	chr15:55881187-55881197
2	MAX	chr15:55879580-55881366	A549	lung:	n/a	chr15:55881187-55881197
3	MAZ	chr15:55878747-55881342	IMR90	lung:	n/a	chr15:55881187-55881197
4	POLR2A	chr15:55879736-55881123	A549	lung:	n/a	n/a
5	MAX	chr15:55880719-55881287	ECC-1	luminal epithelium:	n/a	chr15:55881187-55881197
6	E2F6	chr15:55879701-55881371	A549	lung:	n/a	chr15:55880140-55880150 chr15:55880616-55880628
7	GATA2	chr15:55880489-55881928	SH-SY5Y	brain:	n/a	n/a
8	E2F6	chr15:55880760-55881261	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr15:55879998-55881115	Gliobla	brain:	n/a	n/a
10	POLR2A	chr15:55879530-55881189	H1-neurons	neurons:	n/a	n/a
11	MAX	chr15:55880816-55881287	H1-hESC	embryonic stem cell:	n/a	chr15:55881187-55881197
12	MAX	chr15:55878959-55881445	A549	lung:	n/a	chr15:55881187-55881197
13	POLR2A	chr15:55880324-55881183	SK-N-MC	brain:	n/a	n/a
14	BACH1	chr15:55880445-55881363	H1-hESC	embryonic stem cell:	n/a	n/a
15	HA-E2F1	chr15:55880428-55881183	MCF-7	breast:	n/a	chr15:55880616-55880628
16	TCF12	chr15:55880349-55881432	A549	lung:	n/a	chr15:55880447-55880457
17	MAX	chr15:55880925-55881162	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr15:55880619-55881214	HepG2	liver:	n/a	chr15:55881187-55881197
19	GTF2F1	chr15:55880953-55881142	H1-hESC	embryonic stem cell:	n/a	n/a
20	REST	chr15:55879566-55881383	H1-neurons	neurons:	n/a	chr15:55880207-55880220 chr15:55879940-55879949
21	ZNF143	chr15:55880923-55881504	H1-hESC	embryonic stem cell:	n/a	chr15:55881182-55881200
22	MAX	chr15:55879739-55881320	SK-N-SH	brain:	n/a	chr15:55881187-55881197
23	POLR2A	chr15:55880330-55881223	IMR90	lung:	n/a	n/a
24	MAX	chr15:55880720-55881186	H1-hESC	embryonic stem cell:	n/a	n/a
25	SIN3A	chr15:55880834-55881168	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr15:55879795-55881222	A549	lung:	n/a	chr15:55881187-55881197
27	MXI1	chr15:55879590-55881469	IMR90	lung:	n/a	n/a
28	MAX	chr15:55879731-55881209	HepG2	liver:	n/a	chr15:55881187-55881197
29	E2F6	chr15:55880725-55881271	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr15:55880328-55881245	H1-neurons	neurons:	n/a	n/a
31	MAX	chr15:55880700-55881354	SK-N-SH	brain:	n/a	chr15:55881187-55881197
32	E2F6	chr15:55879767-55881175	A549	lung:	n/a	chr15:55880140-55880150 chr15:55880616-55880628

(count:244 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:55881075-55881125	AG09309	skin:	n/a
2	chr15:55881089-55881139	H1-hESC	embryonic stem cell:	embryo
3	chr15:55881089-55881139	Hela-S3	cervix:	n/a
4	chr15:55881083-55881133	SK-N-SH_RA	brain:	n/a
5	chr15:55881081-55881131	AoSMC	blood vessel:	n/a
6	chr15:55881075-55881125	HCPEpiC	choroid plexus:	n/a
7	chr15:55881083-55881133	CMK	blood:	n/a
8	chr15:55881089-55881139	RPTEC	kidney:	n/a
9	chr15:55881089-55881139	HEK293	kidney:	embryo
10	chr15:55881081-55881131	BJ	skin:	n/a
11	chr15:55881075-55881125	NHDF-neo	bronchial:	n/a
12	chr15:55881081-55881131	NHBE	bronchial:	n/a
13	chr15:55881083-55881133	Jurkat	blood:	n/a
14	chr15:55881081-55881131	PANC-1	pancreas:	n/a
15	chr15:55881083-55881133	AG10803	skin:	n/a
16	chr15:55881075-55881125	AG04449	skin:	fetal
17	chr15:55881081-55881131	HCF	heart:	n/a
18	chr15:55881081-55881131	IMR90	lung:	fetal
19	chr15:55881075-55881125	AG04450	lung:	fetal
20	chr15:55881075-55881125	HNPCEpiC	eye:	n/a
21	chr15:55881083-55881133	GM12892	blood:	n/a
22	chr15:55881081-55881131	Hela-S3	cervix:	n/a
23	chr15:55881075-55881125	SK-N-SH_RA	brain:	n/a
24	chr15:55881075-55881125	SK-N-MC	brain:	n/a
25	chr15:55881075-55881125	IMR90	lung:	fetal
26	chr15:55881083-55881133	HRE	kidney:	n/a
27	chr15:55881083-55881133	ECC-1	luminal epithelium:	n/a
28	chr15:55881083-55881133	AG09309	skin:	n/a
29	chr15:55881075-55881125	U87	brain:	n/a
30	chr15:55881081-55881131	RPTEC	kidney:	n/a
31	chr15:55881075-55881125	CMK	blood:	n/a
32	chr15:55881089-55881139	HRPEpiC	eye:	n/a
33	chr15:55881083-55881133	HUVEC	blood vessel:	n/a
34	chr15:55881075-55881125	NT2-D1	testis:	n/a
35	chr15:55881081-55881131	AG04449	skin:	fetal
36	chr15:55881089-55881139	HRCEpiC	kidney:	n/a
37	chr15:55881089-55881139	GM19239	blood:	n/a
38	chr15:55881083-55881133	NH-A	brain:	n/a
39	chr15:55881089-55881139	HIPEpiC	eye:	n/a
40	chr15:55881075-55881125	HL-60	blood:	n/a
41	chr15:55881089-55881139	Caco-2	colon:	n/a
42	chr15:55881075-55881125	LNCaP	prostate:	n/a
43	chr15:55881075-55881125	H1-hESC	embryonic stem cell:	embryo
44	chr15:55881083-55881133	BJ	skin:	n/a
45	chr15:55881083-55881133	IMR90	lung:	fetal
46	chr15:55881081-55881131	GM12891	blood:	n/a
47	chr15:55881081-55881131	BE2_C	brain:	n/a
48	chr15:55881089-55881139	GM12891	blood:	n/a
49	chr15:55881081-55881131	HL-60	blood:	n/a
50	chr15:55881083-55881133	AG04450	lung:	fetal

No data

Variant related genes	Relation type
PYGO1	TF binding region
PYGO1	CpG island

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12898968	1.00[ASN][1000 genomes]
rs12908925	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513637	1.00[ASN][1000 genomes]
rs652729	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv833016	chr15:55749169-55897906	Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv569540	chr15:55866065-55950082	Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	esv3373041	chr15:55878885-55882033	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
13	esv3328504	chr15:55879460-55881833	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55877400-55881600	Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr15:55878400-55881600	Active TSS	Stomach Smooth Muscle	stomach
3	chr15:55878400-55881800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr15:55878800-55881400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
5	chr15:55878800-55881600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr15:55878800-55881600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:55878800-55881800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:55879000-55881200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:55879000-55881400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:55879000-55881400	Active TSS	Psoas Muscle	Psoas
11	chr15:55879000-55881600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:55879000-55881600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
13	chr15:55879000-55881600	Active TSS	Ovary	ovary
14	chr15:55879000-55881600	Active TSS	HSMM	muscle
15	chr15:55879200-55881200	Active TSS	Muscle Satellite Cultured Cells	--
16	chr15:55879200-55881200	Active TSS	A549	lung
17	chr15:55879200-55881400	Active TSS	Fetal Stomach	stomach
18	chr15:55879200-55881400	Active TSS	NHLF	lung
19	chr15:55879200-55881600	Active TSS	NH-A	brain
20	chr15:55879200-55881800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:55879200-55881800	Active TSS	NHDF-Ad	bronchial
22	chr15:55879400-55881200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr15:55879400-55881200	Active TSS	Brain Germinal Matrix	brain
24	chr15:55879400-55881200	Active TSS	Placenta Amnion	Placenta Amnion
25	chr15:55879400-55881400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr15:55879400-55881400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr15:55879400-55881400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr15:55879400-55881400	Active TSS	Aorta	Aorta
29	chr15:55879400-55881400	Active TSS	Brain Anterior Caudate	brain
30	chr15:55879400-55881400	Active TSS	Colon Smooth Muscle	Colon
31	chr15:55879400-55881400	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr15:55879400-55881400	Active TSS	Right Atrium	heart
33	chr15:55879400-55881400	Active TSS	Right Ventricle	heart
34	chr15:55879400-55881600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
35	chr15:55879400-55881600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:55879400-55881600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
37	chr15:55879400-55881600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
38	chr15:55879400-55881600	Active TSS	Fetal Kidney	kidney
39	chr15:55879400-55881600	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr15:55879400-55881800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:55879400-55881800	Active TSS	Osteobl	bone
42	chr15:55879600-55881200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr15:55879600-55881200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:55879600-55881200	Active TSS	Fetal Brain Female	brain
45	chr15:55879600-55881200	Active TSS	Gastric	stomach
46	chr15:55879600-55881200	Active TSS	Pancreas	Pancrea
47	chr15:55879600-55881400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr15:55879600-55881400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
49	chr15:55879600-55881400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:55879600-55881400	Active TSS	Fetal Lung	lung

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