Variant report

Variant	rs538560729
Chromosome Location	chr15:52404270-52404271
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:52404245-52404590	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr15:52404006-52405001	H1-hESC	embryonic stem cell:	n/a	chr15:52404011-52404018 chr15:52404974-52404983
3	POLR2A	chr15:52403762-52405802	NB4	blood:	n/a	n/a
4	POLR2A	chr15:52403715-52405006	GM19193	blood:	n/a	n/a
5	EBF1	chr15:52404136-52404655	GM12878	blood:	n/a	n/a
6	CTCF	chr15:52404260-52404410	GM12867	blood:	n/a	n/a
7	YY1	chr15:52403922-52405027	GM12878	blood:	n/a	chr15:52404972-52404986 chr15:52404061-52404071
8	POLR2A	chr15:52403564-52404976	GM12891	blood:	n/a	n/a
9	MAX	chr15:52404172-52404728	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr15:52403861-52404544	NB4	blood:	n/a	n/a
11	POLR2A	chr15:52404074-52404336	GM12891	blood:	n/a	n/a
12	POLR2A	chr15:52404206-52404973	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:52404092-52404988	GM12878	blood:	n/a	n/a
14	MAX	chr15:52404100-52404834	MCF-7	breast:	n/a	n/a
15	MTA3	chr15:52403416-52404901	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:52404242-52404968	GM12878	blood:	n/a	n/a
17	E2F4	chr15:52404148-52404298	GM12878	blood:	n/a	n/a
18	MAX	chr15:52404172-52404998	MCF-7	breast:	n/a	n/a
19	ELF1	chr15:52403663-52404665	GM12878	blood:	n/a	n/a
20	E2F6	chr15:52404214-52404897	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr15:52404255-52404872	GM12878	blood:	n/a	n/a
22	YY1	chr15:52403803-52404283	GM12891	blood:	n/a	chr15:52404061-52404071
23	MAX	chr15:52404148-52404873	H1-hESC	embryonic stem cell:	n/a	n/a
24	PML	chr15:52403631-52404813	GM12878	blood:	n/a	n/a
25	YY1	chr15:52403896-52404994	GM12878	blood:	n/a	chr15:52404972-52404986 chr15:52404061-52404071
26	POLR2A	chr15:52403681-52404911	GM12891	blood:	n/a	n/a
27	STAT1	chr15:52404196-52404296	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:52403797-52404959	GM12891	blood:	n/a	n/a
29	TCF3	chr15:52404270-52404789	GM12878	blood:	n/a	n/a
30	MAX	chr15:52404201-52404300	NB4	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:52404232-52404282	MCF-7	breast:	n/a
2	chr15:52404232-52404282	NH-A	brain:	n/a
3	chr15:52404232-52404282	Jurkat	blood:	n/a
4	chr15:52404232-52404282	BE2_C	brain:	n/a
5	chr15:52404232-52404282	U87	brain:	n/a
6	chr15:52404232-52404282	AG09319	gingival:	n/a
7	chr15:52404232-52404282	GM12878	blood:	n/a
8	chr15:52404232-52404282	ovcar-3	ovarian:	n/a
9	chr15:52404232-52404282	SKMC	muscle:	n/a
10	chr15:52404232-52404282	NB4	blood:	n/a
11	chr15:52404232-52404282	SAEC	small airway:	n/a
12	chr15:52404232-52404282	K562	blood:	n/a
13	chr15:52404232-52404282	GM12891	blood:	n/a
14	chr15:52404232-52404282	HepG2	liver:	n/a
15	chr15:52404232-52404282	CMK	blood:	n/a
16	chr15:52404232-52404282	GM06990	blood:	n/a
17	chr15:52404232-52404282	HMEC	breast:	n/a
18	chr15:52404232-52404282	HEEpiC	esophagus:	n/a
19	chr15:52404232-52404282	Caco-2	colon:	n/a
20	chr15:52404232-52404282	NT2-D1	testis:	n/a
21	chr15:52404232-52404282	A549	lung:	n/a
22	chr15:52404232-52404282	PANC-1	pancreas:	n/a
23	chr15:52404232-52404282	AoSMC	blood vessel:	n/a
24	chr15:52404232-52404282	HRPEpiC	eye:	n/a
25	chr15:52404232-52404282	HNPCEpiC	eye:	n/a
26	chr15:52404232-52404282	SK-N-MC	brain:	n/a
27	chr15:52404232-52404282	HCF	heart:	n/a
28	chr15:52404232-52404282	MCF10A-Er-Src	breast:	n/a
29	chr15:52404232-52404282	IMR90	lung:	fetal
30	chr15:52404232-52404282	HAEpiC	amniotic membrane:	n/a
31	chr15:52404232-52404282	LNCaP	prostate:	n/a
32	chr15:52404232-52404282	HUVEC	blood vessel:	n/a
33	chr15:52404232-52404282	ECC-1	luminal epithelium:	n/a
34	chr15:52404232-52404282	BJ	skin:	n/a
35	chr15:52404232-52404282	Hela-S3	cervix:	n/a
36	chr15:52404232-52404282	SK-N-SH_RA	brain:	n/a
37	chr15:52404232-52404282	NHBE	bronchial:	n/a
38	chr15:52404232-52404282	PrEC	prostate:	n/a
39	chr15:52404232-52404282	T-47D	breast:	n/a
40	chr15:52404232-52404282	AG10803	skin:	n/a
41	chr15:52404232-52404282	GM19239	blood:	n/a
42	chr15:52404232-52404282	RPTEC	kidney:	n/a
43	chr15:52404232-52404282	AG04450	lung:	fetal
44	chr15:52404232-52404282	SK-N-SH	brain:	n/a
45	chr15:52404232-52404282	HPAEpiC	pulmonary alveolar:	n/a
46	chr15:52404232-52404282	HCPEpiC	choroid plexus:	n/a
47	chr15:52404232-52404282	AG04449	skin:	fetal
48	chr15:52404232-52404282	HCM	heart:	n/a
49	chr15:52404232-52404282	HIPEpiC	eye:	n/a
50	chr15:52404232-52404282	H1-hESC	embryonic stem cell:	embryo

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52263208..52265625-chr15:52404085..52407650,4	MCF-7	breast:
2	chr15:52393212..52395889-chr15:52402587..52404691,2	K562	blood:
3	chr15:52403961..52406655-chr15:52470750..52472609,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259327	TF binding region
ENSG00000259327	CpG island
ENSG00000259577	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv3412125	chr15:52404008-52404454	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52402200-52411400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:52402400-52405600	Weak transcription	HepG2	liver
3	chr15:52403600-52404800	Flanking Active TSS	GM12878-XiMat	blood
4	chr15:52403800-52404400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:52403800-52404400	Bivalent Enhancer	Fetal Intestine Small	intestine
6	chr15:52404000-52404400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:52404000-52404400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr15:52404000-52404400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr15:52404000-52404400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:52404000-52404400	Enhancers	Liver	Liver
11	chr15:52404000-52404400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr15:52404000-52404400	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr15:52404000-52404400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
14	chr15:52404000-52404400	Enhancers	Right Ventricle	heart
15	chr15:52404000-52404400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr15:52404000-52404600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:52404000-52404600	Flanking Active TSS	Colonic Mucosa	Colon
18	chr15:52404000-52405000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr15:52404000-52405000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr15:52404000-52405000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:52404000-52405000	Active TSS	Brain Angular Gyrus	brain
22	chr15:52404000-52405000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
23	chr15:52404000-52405000	Active TSS	Esophagus	oesophagus
24	chr15:52404000-52405000	Bivalent Enhancer	Placenta	Placenta
25	chr15:52404000-52405000	Enhancers	Gastric	stomach
26	chr15:52404000-52405000	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr15:52404000-52405400	Enhancers	Spleen	Spleen
28	chr15:52404200-52404400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
29	chr15:52404200-52404400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
30	chr15:52404200-52404400	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr15:52404200-52404400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr15:52404200-52404400	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:52404200-52404400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr15:52404200-52404400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
35	chr15:52404200-52404400	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
36	chr15:52404200-52404400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
37	chr15:52404200-52404400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:52404200-52404400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
39	chr15:52404200-52404400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:52404200-52404400	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
41	chr15:52404200-52404400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:52404200-52404400	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr15:52404200-52404400	Bivalent Enhancer	Fetal Stomach	stomach
44	chr15:52404200-52404400	Bivalent Enhancer	Fetal Thymus	thymus
45	chr15:52404200-52404400	Bivalent Enhancer	Left Ventricle	heart
46	chr15:52404200-52404400	Bivalent Enhancer	Lung	lung
47	chr15:52404200-52404400	Enhancers	Pancreas	Pancrea
48	chr15:52404200-52404400	Enhancers	Psoas Muscle	Psoas
49	chr15:52404200-52404400	Flanking Active TSS	Right Atrium	heart
50	chr15:52404200-52404400	Bivalent Enhancer	Stomach Mucosa	stomach

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