Variant report

Variant	rs1509408
Chromosome Location	chr15:56286313-56286314
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:117)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:117 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:56286260-56286410	HFF	foreskin:	n/a	n/a
2	RAD21	chr15:56286170-56286871	HCT-116	colon:	n/a	chr15:56286556-56286575
3	RAD21	chr15:56286232-56286648	A549	lung:	n/a	chr15:56286556-56286575
4	CTCF	chr15:56286260-56286410	GM12873	blood:	n/a	n/a
5	UBTF	chr15:56285096-56286689	K562	blood:	n/a	n/a
6	CTCF	chr15:56286200-56286350	Hela-S3	cervix:	n/a	n/a
7	CHD2	chr15:56286224-56286581	H1-hESC	embryonic stem cell:	n/a	n/a
8	TBP	chr15:56285276-56286643	K562	blood:	n/a	n/a
9	FOXA2	chr15:56286283-56286578	HepG2	liver:	n/a	n/a
10	MXI1	chr15:56285179-56286589	Hela-S3	cervix:	n/a	n/a
11	SIN3AK20	chr15:56285017-56286778	MCF-7	breast:	n/a	n/a
12	GATA3	chr15:56285145-56286502	A549	lung:	n/a	chr15:56285373-56285383
13	POLR2A	chr15:56285156-56286697	Hela-S3	cervix:	n/a	n/a
14	RCOR1	chr15:56285227-56286553	HepG2	liver:	n/a	n/a
15	RAD21	chr15:56286249-56286719	A549	lung:	n/a	chr15:56286556-56286575
16	POLR2A	chr15:56285188-56286430	U87	brain:	n/a	n/a
17	POLR2A	chr15:56285233-56286708	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr15:56285212-56286684	K562	blood:	n/a	n/a
19	REST	chr15:56285413-56286778	H1-neurons	neurons:	n/a	chr15:56285589-56285602
20	TAF1	chr15:56286100-56286618	PFSK-1	brain:	n/a	n/a
21	SIN3A	chr15:56285115-56286642	H1-hESC	embryonic stem cell:	n/a	chr15:56285681-56285692 chr15:56285525-56285534
22	EP300	chr15:56285153-56286372	SK-N-SH	brain:	n/a	chr15:56285518-56285534 chr15:56285524-56285540 chr15:56285462-56285471 chr15:56285629-56285638
23	POLR2A	chr15:56285142-56286725	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr15:56285096-56286796	SK-N-SH	brain:	n/a	chr15:56286558-56286571 chr15:56286555-56286573 chr15:56286557-56286578
25	POLR2A	chr15:56285194-56286694	HepG2	liver:	n/a	n/a
26	RCOR1	chr15:56285091-56287129	Hela-S3	cervix:	n/a	n/a
27	TEAD4	chr15:56286152-56286713	K562	blood:	n/a	n/a
28	POLR2A	chr15:56285226-56286362	HepG2	liver:	n/a	n/a
29	RCOR1	chr15:56284111-56286676	IMR90	lung:	n/a	n/a
30	CTCF	chr15:56286220-56286370	GM12865	blood:	n/a	n/a
31	CTCF	chr15:56286292-56286729	K562	blood:	n/a	chr15:56286558-56286571 chr15:56286555-56286573 chr15:56286557-56286578
32	JUND	chr15:56285513-56286459	A549	lung:	n/a	chr15:56285680-56285689
33	MXI1	chr15:56284236-56286734	IMR90	lung:	n/a	n/a
34	CEBPB	chr15:56285035-56287150	Hela-S3	cervix:	n/a	chr15:56286825-56286838 chr15:56286689-56286697
35	MYC	chr15:56285335-56286539	K562	blood:	n/a	chr15:56285420-56285430
36	SIN3AK20	chr15:56285135-56286505	SK-N-SH	brain:	n/a	n/a
37	TCF12	chr15:56285114-56286564	A549	lung:	n/a	chr15:56286428-56286437
38	MAZ	chr15:56285162-56286678	Hela-S3	cervix:	n/a	chr15:56285420-56285430
39	POLR2A	chr15:56285509-56286320	H1-neurons	neurons:	n/a	n/a
40	MAFK	chr15:56286199-56286370	HepG2	liver:	n/a	n/a
41	CTCF	chr15:56286200-56286350	AG04450	lung:	n/a	n/a
42	UBTF	chr15:56285108-56286636	K562	blood:	n/a	n/a
43	CTCF	chr15:56286240-56286390	GM12867	blood:	n/a	n/a
44	POLR2A	chr15:56285219-56286469	A549	lung:	n/a	n/a
45	TBL1XR1	chr15:56286188-56286975	K562	blood:	n/a	n/a
46	MAZ	chr15:56284977-56286862	IMR90	lung:	n/a	chr15:56285420-56285430
47	CTCF	chr15:56284876-56286986	A549	lung:	n/a	chr15:56286558-56286571 chr15:56286555-56286573 chr15:56286557-56286578
48	POLR2A	chr15:56285158-56286686	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr15:56285180-56286678	Hela-S3	cervix:	n/a	n/a
50	SMARCB1	chr15:56285180-56287094	Hela-S3	cervix:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:56286283-56286333	U87	brain:	n/a
2	chr15:56286283-56286333	NT2-D1	testis:	n/a
3	chr15:56286283-56286333	MCF10A-Er-Src	breast:	n/a
4	chr15:56286283-56286333	SAEC	small airway:	n/a
5	chr15:56286283-56286333	SK-N-SH_RA	brain:	n/a
6	chr15:56286283-56286333	AG09319	gingival:	n/a
7	chr15:56286283-56286333	GM06990	blood:	n/a
8	chr15:56286283-56286333	LNCaP	prostate:	n/a
9	chr15:56286283-56286333	Hela-S3	cervix:	n/a
10	chr15:56286283-56286333	MCF-7	breast:	n/a
11	chr15:56286283-56286333	ovcar-3	ovarian:	n/a
12	chr15:56286283-56286333	GM12892	blood:	n/a
13	chr15:56286283-56286333	PrEC	prostate:	n/a
14	chr15:56286283-56286333	PFSK-1	brain:	n/a
15	chr15:56286283-56286333	HEEpiC	esophagus:	n/a
16	chr15:56286283-56286333	GM12878	blood:	n/a
17	chr15:56286283-56286333	NHBE	bronchial:	n/a
18	chr15:56286283-56286333	RPTEC	kidney:	n/a
19	chr15:56286283-56286333	HL-60	blood:	n/a
20	chr15:56286283-56286333	SK-N-SH	brain:	n/a
21	chr15:56286283-56286333	NH-A	brain:	n/a
22	chr15:56286283-56286333	AG10803	skin:	n/a
23	chr15:56286283-56286333	HCT-116	colon:	n/a
24	chr15:56286283-56286333	SK-N-MC	brain:	n/a
25	chr15:56286283-56286333	HRPEpiC	eye:	n/a
26	chr15:56286283-56286333	SKMC	muscle:	n/a
27	chr15:56286283-56286333	GM12891	blood:	n/a
28	chr15:56286283-56286333	AG04449	skin:	fetal
29	chr15:56286283-56286333	NHDF-neo	bronchial:	n/a
30	chr15:56286283-56286333	GM19239	blood:	n/a
31	chr15:56286283-56286333	HUVEC	blood vessel:	n/a
32	chr15:56286283-56286333	H1-hESC	embryonic stem cell:	embryo
33	chr15:56286283-56286333	HAEpiC	amniotic membrane:	n/a
34	chr15:56286283-56286333	BJ	skin:	n/a
35	chr15:56286283-56286333	A549	lung:	n/a
36	chr15:56286283-56286333	HepG2	liver:	n/a
37	chr15:56286283-56286333	HPAEpiC	pulmonary alveolar:	n/a
38	chr15:56286283-56286333	PANC-1	pancreas:	n/a
39	chr15:56286283-56286333	Jurkat	blood:	n/a
40	chr15:56286283-56286333	HRE	kidney:	n/a
41	chr15:56286283-56286333	HCPEpiC	choroid plexus:	n/a
42	chr15:56286283-56286333	HNPCEpiC	eye:	n/a
43	chr15:56286283-56286333	HRCEpiC	kidney:	n/a
44	chr15:56286283-56286333	ProgFib	skin:	n/a
45	chr15:56286283-56286333	AG04450	lung:	fetal
46	chr15:56286283-56286333	K562	blood:	n/a
47	chr15:56286283-56286333	IMR90	lung:	fetal
48	chr15:56286283-56286333	T-47D	breast:	n/a
49	chr15:56286283-56286333	HCM	heart:	n/a
50	chr15:56286283-56286333	ECC-1	luminal epithelium:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:56286056..56286943-chr15:56344508..56345311,2	MCF-7	breast:
2	chr15:56286068..56286594-chr15:56344895..56345645,2	MCF-7	breast:
3	chr1:152008878..152009756-chr15:56285598..56286362,2	Hela-S3	cervix:
4	chr15:56285803..56286769-chr7:144532503..144533132,2	HCT-116	colon:
5	chr15:56285985..56288747-chr15:56326549..56330061,4	MCF-7	breast:
6	chr15:56285724..56286656-chr8:8559373..8559873,2	Hela-S3	cervix:
7	chr1:145381291..145384278-chr15:56284107..56286728,2	MCF-7	breast:
8	chr15:56285499..56287418-chr15:56534884..56536553,2	K562	blood:
9	chr15:56284455..56287261-chr15:56299264..56302045,2	MCF-7	breast:
10	chr15:56282050..56287467-chr15:56534024..56538662,8	MCF-7	breast:
11	chr1:28994985..28995485-chr15:56285972..56286627,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
NEDD4	TF binding region
NEDD4	CpG island
ENSG00000196511	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000162419	Chromatin interaction
ENSG00000181827	Chromatin interaction
ENSG00000176305	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000253958	Chromatin interaction
ENSG00000151575	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000230183	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11635590	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12438057	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2036741	1.00[JPT][hapmap]
rs4144243	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181344	1.00[ASN][1000 genomes]
rs8032922	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904245	chr15:56229760-56324451	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv457159	chr15:56255774-56321854	Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv569543	chr15:56255774-56321854	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv457160	chr15:56273446-56320235	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
6	nsv569544	chr15:56273446-56320235	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
7	nsv457161	chr15:56274443-56324451	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
8	nsv569545	chr15:56274443-56324451	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
9	nsv569546	chr15:56274443-56337527	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56283800-56286800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:56284000-56286800	Active TSS	Right Atrium	heart
3	chr15:56284000-56287000	Active TSS	NHLF	lung
4	chr15:56284200-56286800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:56284200-56286800	Active TSS	Fetal Muscle Trunk	muscle
6	chr15:56284200-56287200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:56284400-56286400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:56284400-56286400	Active TSS	Stomach Smooth Muscle	stomach
9	chr15:56284400-56286400	Active TSS	NHEK	skin
10	chr15:56284400-56286600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:56284400-56286600	Active TSS	Aorta	Aorta
12	chr15:56284400-56286800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:56284400-56286800	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr15:56284600-56286400	Active TSS	Brain Angular Gyrus	brain
15	chr15:56284600-56286400	Active TSS	HSMMtube	muscle
16	chr15:56284600-56286600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:56284600-56286600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:56284600-56286600	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr15:56284600-56286600	Active TSS	A549	lung
20	chr15:56284600-56286800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr15:56284600-56286800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr15:56284600-56286800	Active TSS	Fetal Stomach	stomach
23	chr15:56284600-56286800	Active TSS	Psoas Muscle	Psoas
24	chr15:56284600-56286800	Active TSS	Right Ventricle	heart
25	chr15:56284600-56286800	Active TSS	HSMM	muscle
26	chr15:56284600-56287000	Active TSS	Placenta	Placenta
27	chr15:56284600-56287000	Active TSS	NHDF-Ad	bronchial
28	chr15:56284800-56286400	Active TSS	Primary hematopoietic stem cells	blood
29	chr15:56284800-56286400	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr15:56284800-56286400	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr15:56284800-56286400	Active TSS	Brain Anterior Caudate	brain
32	chr15:56284800-56286400	Active TSS	Brain Hippocampus Middle	brain
33	chr15:56284800-56286400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr15:56284800-56286400	Active TSS	Fetal Lung	lung
35	chr15:56284800-56286400	Active TSS	HMEC	breast
36	chr15:56284800-56286600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:56284800-56286600	Active TSS	Muscle Satellite Cultured Cells	--
38	chr15:56284800-56286600	Active TSS	Ovary	ovary
39	chr15:56284800-56286800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:56284800-56286800	Active TSS	Brain Cingulate Gyrus	brain
41	chr15:56284800-56286800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:56284800-56287000	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr15:56285000-56286400	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr15:56285000-56286400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:56285000-56286400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:56285000-56286400	Active TSS	Liver	Liver
47	chr15:56285000-56286400	Active TSS	Duodenum Mucosa	Duodenum
48	chr15:56285000-56286400	Active TSS	HUVEC	blood vessel
49	chr15:56285000-56286400	Active TSS	NH-A	brain
50	chr15:56285000-56286600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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