Variant report

Variant	rs12909497
Chromosome Location	chr15:55881745-55881746
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr15:55881525-55881813	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr15:55881586-55881812	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr15:55881502-55881792	SK-N-SH_RA	brain:	n/a	n/a
4	GATA2	chr15:55880489-55881928	SH-SY5Y	brain:	n/a	n/a
5	EP300	chr15:55881514-55881910	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr15:55881496-55881829	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr15:55881686-55881922	SH-SY5Y	brain:	n/a	n/a
8	EP300	chr15:55881456-55881907	SK-N-SH_RA	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:55881706-55881756	HIPEpiC	eye:	n/a
2	chr15:55881706-55881756	Hepatocyte	liver:	n/a
3	chr15:55881706-55881756	HepG2	liver:	n/a
4	chr15:55881706-55881756	MCF10A-Er-Src	breast:	n/a
5	chr15:55881706-55881756	HCM	heart:	n/a
6	chr15:55881706-55881756	HEEpiC	esophagus:	n/a
7	chr15:55881706-55881756	H1-hESC	embryonic stem cell:	embryo
8	chr15:55881706-55881756	HCPEpiC	choroid plexus:	n/a
9	chr15:55881706-55881756	CMK	blood:	n/a
10	chr15:55881706-55881756	ProgFib	skin:	n/a
11	chr15:55881706-55881756	BE2_C	brain:	n/a
12	chr15:55881706-55881756	GM06990	blood:	n/a
13	chr15:55881706-55881756	GM19239	blood:	n/a
14	chr15:55881706-55881756	GM12892	blood:	n/a
15	chr15:55881706-55881756	HAEpiC	amniotic membrane:	n/a
16	chr15:55881706-55881756	HCF	heart:	n/a
17	chr15:55881706-55881756	NB4	blood:	n/a
18	chr15:55881706-55881756	Hela-S3	cervix:	n/a
19	chr15:55881706-55881756	SK-N-SH	brain:	n/a
20	chr15:55881706-55881756	HCT-116	colon:	n/a
21	chr15:55881706-55881756	GM12878	blood:	n/a
22	chr15:55881706-55881756	HRE	kidney:	n/a
23	chr15:55881706-55881756	HRPEpiC	eye:	n/a
24	chr15:55881706-55881756	GM12891	blood:	n/a
25	chr15:55881706-55881756	HL-60	blood:	n/a
26	chr15:55881706-55881756	AG04450	lung:	fetal
27	chr15:55881706-55881756	A549	lung:	n/a
28	chr15:55881706-55881756	AoSMC	blood vessel:	n/a
29	chr15:55881706-55881756	U87	brain:	n/a
30	chr15:55881706-55881756	NT2-D1	testis:	n/a
31	chr15:55881706-55881756	NH-A	brain:	n/a
32	chr15:55881706-55881756	AG10803	skin:	n/a
33	chr15:55881706-55881756	MCF-7	breast:	n/a
34	chr15:55881706-55881756	HNPCEpiC	eye:	n/a
35	chr15:55881706-55881756	NHBE	bronchial:	n/a
36	chr15:55881706-55881756	ovcar-3	ovarian:	n/a
37	chr15:55881706-55881756	HRCEpiC	kidney:	n/a
38	chr15:55881706-55881756	K562	blood:	n/a
39	chr15:55881706-55881756	NHDF-neo	bronchial:	n/a
40	chr15:55881706-55881756	PrEC	prostate:	n/a
41	chr15:55881706-55881756	HUVEC	blood vessel:	n/a
42	chr15:55881706-55881756	HPAEpiC	pulmonary alveolar:	n/a
43	chr15:55881706-55881756	PFSK-1	brain:	n/a
44	chr15:55881706-55881756	HEK293	kidney:	embryo
45	chr15:55881706-55881756	AG09319	gingival:	n/a
46	chr15:55881706-55881756	IMR90	lung:	fetal
47	chr15:55881706-55881756	AG09309	skin:	n/a
48	chr15:55881706-55881756	Caco-2	colon:	n/a
49	chr15:55881706-55881756	SAEC	small airway:	n/a
50	chr15:55881706-55881756	LNCaP	prostate:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-178D12.1.1-5	chr15:55881501-55882082	NONHSAT044003

No data

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

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1011061	1.00[CHB][hapmap]
rs11852746	1.00[CHB][hapmap]
rs12899976	1.00[CHB][hapmap]
rs12908232	1.00[CHB][hapmap]
rs1550326	1.00[CHB][hapmap]
rs3985768	1.00[CHB][hapmap]
rs4774222	1.00[CHB][hapmap]
rs491014	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs530798	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8028880	1.00[CHB][hapmap]
rs8036481	1.00[CHB][hapmap]
rs934886	1.00[CHB][hapmap]
rs9920546	1.00[CHB][hapmap]

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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55878400-55881800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr15:55878800-55881800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:55879200-55881800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:55879200-55881800	Active TSS	NHDF-Ad	bronchial
5	chr15:55879400-55881800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:55879400-55881800	Active TSS	Osteobl	bone
7	chr15:55879800-55882000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:55880800-55881800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:55880800-55881800	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
10	chr15:55881200-55881800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:55881200-55881800	Active TSS	Colonic Mucosa	Colon
12	chr15:55881200-55881800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
13	chr15:55881200-55881800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
14	chr15:55881200-55881800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
15	chr15:55881400-55881800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:55881400-55881800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
17	chr15:55881400-55881800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:55881400-55881800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:55881400-55881800	Enhancers	Brain Anterior Caudate	brain
20	chr15:55881400-55881800	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr15:55881400-55881800	Active TSS	Fetal Brain Male	brain
22	chr15:55881400-55881800	Flanking Active TSS	Fetal Lung	lung
23	chr15:55881400-55881800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
24	chr15:55881400-55881800	Enhancers	Right Ventricle	heart
25	chr15:55881400-55882000	Enhancers	Placenta	Placenta
26	chr15:55881600-55881800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:55881600-55881800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:55881600-55881800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
29	chr15:55881600-55881800	Active TSS	Muscle Satellite Cultured Cells	--
30	chr15:55881600-55881800	Enhancers	Fetal Brain Female	brain
31	chr15:55881600-55881800	Enhancers	Fetal Heart	heart
32	chr15:55881600-55881800	Flanking Active TSS	Fetal Kidney	kidney
33	chr15:55881600-55881800	Enhancers	Ovary	ovary
34	chr15:55881600-55881800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
35	chr15:55881600-55881800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr15:55881600-55881800	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr15:55881600-55881800	Active TSS	HSMMtube	muscle
38	chr15:55881600-55882000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:55881600-55882000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:55881600-55882000	Enhancers	Psoas Muscle	Psoas
41	chr15:55881600-55882000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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