Variant report

Variant	rs542038034
Chromosome Location	chr15:55880381-55880382
allele	-/CGC/GCCGC
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	POLR2A	chr15:55880289-55880684	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:55879868-55880722	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr15:55880097-55880970	HUVEC	blood vessel:	n/a	n/a
4	MAX	chr15:55879713-55881300	ECC-1	luminal epithelium:	n/a	chr15:55881187-55881197
5	POLR2A	chr15:55880025-55880872	HepG2	liver:	n/a	n/a
6	MAX	chr15:55879580-55881366	A549	lung:	n/a	chr15:55881187-55881197
7	MAX	chr15:55879746-55880440	HepG2	liver:	n/a	n/a
8	MAZ	chr15:55878747-55881342	IMR90	lung:	n/a	chr15:55881187-55881197
9	POLR2A	chr15:55879736-55881123	A549	lung:	n/a	n/a
10	MAX	chr15:55880324-55880678	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr15:55880295-55880645	SK-N-MC	brain:	n/a	n/a
12	E2F6	chr15:55879701-55881371	A549	lung:	n/a	chr15:55880140-55880150 chr15:55880616-55880628
13	POLR2A	chr15:55879851-55881051	A549	lung:	n/a	n/a
14	RAD21	chr15:55880311-55880615	SK-N-SH_RA	brain:	n/a	n/a
15	E2F4	chr15:55879896-55880543	MCF10A-Er-Src	breast:	n/a	chr15:55880140-55880150
16	TAF1	chr15:55880289-55880633	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr15:55880360-55880510	AG09319	gingival:	n/a	n/a
18	E2F6	chr15:55880290-55880493	K562	blood:	n/a	n/a
19	MAX	chr15:55879773-55880633	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr15:55879973-55881037	A549	lung:	n/a	n/a
21	YY1	chr15:55880296-55880654	SK-N-SH_RA	brain:	n/a	chr15:55880583-55880594 chr15:55880631-55880642
22	POLR2A	chr15:55879998-55881115	Gliobla	brain:	n/a	n/a
23	SIN3AK20	chr15:55880307-55880678	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr15:55880359-55880646	U87	brain:	n/a	n/a
25	POLR2A	chr15:55879530-55881189	H1-neurons	neurons:	n/a	n/a
26	CTCF	chr15:55880380-55880530	HRE	kidney:	n/a	n/a
27	CTCF	chr15:55880380-55880530	NHEK	skin:	n/a	n/a
28	MAX	chr15:55878959-55881445	A549	lung:	n/a	chr15:55881187-55881197
29	POLR2A	chr15:55880331-55880665	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr15:55879769-55881032	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr15:55879713-55880722	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr15:55880324-55881183	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr15:55880318-55881012	HUVEC	blood vessel:	n/a	n/a
34	TCF12	chr15:55880349-55881432	A549	lung:	n/a	chr15:55880447-55880457
35	TCF7L2	chr15:55879604-55880549	HEK293	kidney:	n/a	chr15:55880126-55880140 chr15:55880125-55880141 chr15:55880125-55880141
36	TAF1	chr15:55879930-55880707	ECC-1	luminal epithelium:	n/a	n/a
37	JUND	chr15:55879960-55881057	A549	lung:	n/a	chr15:55879988-55879999
38	TAF1	chr15:55880292-55880818	H1-neurons	neurons:	n/a	n/a
39	TAF1	chr15:55880330-55880670	H1-neurons	neurons:	n/a	n/a
40	POLR2A	chr15:55880325-55880947	SK-N-SH	brain:	n/a	n/a
41	TAF1	chr15:55880326-55880653	H1-hESC	embryonic stem cell:	n/a	n/a
42	EGR1	chr15:55880290-55880481	K562	blood:	n/a	n/a
43	POLR2A	chr15:55880038-55880983	A549	lung:	n/a	n/a
44	E2F6	chr15:55879761-55880702	H1-hESC	embryonic stem cell:	n/a	chr15:55880140-55880150 chr15:55880616-55880628
45	POLR2A	chr15:55880320-55880685	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr15:55880303-55880656	ECC-1	luminal epithelium:	n/a	n/a
47	NR3C1	chr15:55879992-55881054	A549	lung:	n/a	n/a
48	REST	chr15:55879566-55881383	H1-neurons	neurons:	n/a	chr15:55880207-55880220 chr15:55879940-55879949
49	POLR2A	chr15:55880073-55880983	A549	lung:	n/a	n/a
50	TAF1	chr15:55880275-55880625	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
PYGO1	TF binding region

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

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:119 , 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	chr15:55879000-55881000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
9	chr15:55879000-55881200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:55879000-55881400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:55879000-55881400	Active TSS	Psoas Muscle	Psoas
12	chr15:55879000-55881600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:55879000-55881600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr15:55879000-55881600	Active TSS	Ovary	ovary
15	chr15:55879000-55881600	Active TSS	HSMM	muscle
16	chr15:55879200-55881000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:55879200-55881000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
18	chr15:55879200-55881000	Active TSS	Fetal Muscle Leg	muscle
19	chr15:55879200-55881200	Active TSS	Muscle Satellite Cultured Cells	--
20	chr15:55879200-55881200	Active TSS	A549	lung
21	chr15:55879200-55881400	Active TSS	Fetal Stomach	stomach
22	chr15:55879200-55881400	Active TSS	NHLF	lung
23	chr15:55879200-55881600	Active TSS	NH-A	brain
24	chr15:55879200-55881800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:55879200-55881800	Active TSS	NHDF-Ad	bronchial
26	chr15:55879400-55880400	Bivalent/Poised TSS	NHEK	skin
27	chr15:55879400-55880800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:55879400-55881200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
29	chr15:55879400-55881200	Active TSS	Brain Germinal Matrix	brain
30	chr15:55879400-55881200	Active TSS	Placenta Amnion	Placenta Amnion
31	chr15:55879400-55881400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr15:55879400-55881400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr15:55879400-55881400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr15:55879400-55881400	Active TSS	Aorta	Aorta
35	chr15:55879400-55881400	Active TSS	Brain Anterior Caudate	brain
36	chr15:55879400-55881400	Active TSS	Colon Smooth Muscle	Colon
37	chr15:55879400-55881400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr15:55879400-55881400	Active TSS	Right Atrium	heart
39	chr15:55879400-55881400	Active TSS	Right Ventricle	heart
40	chr15:55879400-55881600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr15:55879400-55881600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:55879400-55881600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr15:55879400-55881600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
44	chr15:55879400-55881600	Active TSS	Fetal Kidney	kidney
45	chr15:55879400-55881600	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr15:55879400-55881800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:55879400-55881800	Active TSS	Osteobl	bone
48	chr15:55879600-55881000	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr15:55879600-55881000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
50	chr15:55879600-55881000	Active TSS	Brain Inferior Temporal Lobe	brain

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