Variant report

Variant	rs59824250
Chromosome Location	chr15:78469740-78469741
allele	C/T
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	CTCF	chr15:78469708-78470070	HepG2	liver:	n/a	chr15:78469893-78469909
2	ZNF143	chr15:78469737-78470092	H1-hESC	embryonic stem cell:	n/a	chr15:78469979-78469997
3	CTCF	chr15:78469685-78470105	K562	blood:	n/a	chr15:78469893-78469909
4	RAD21	chr15:78469730-78470098	A549	lung:	n/a	n/a
5	CTCF	chr15:78469662-78470254	K562	blood:	n/a	chr15:78469893-78469909
6	RAD21	chr15:78469582-78470309	ECC-1	luminal epithelium:	n/a	n/a
7	RAD21	chr15:78469560-78470370	MCF-7	breast:	n/a	n/a
8	YY1	chr15:78469711-78470051	A549	lung:	n/a	chr15:78469901-78469910
9	MAZ	chr15:78469733-78470056	K562	blood:	n/a	n/a
10	CTCF	chr15:78469731-78470112	ECC-1	luminal epithelium:	n/a	chr15:78469893-78469909
11	RAD21	chr15:78469682-78470058	SK-N-SH_RA	brain:	n/a	n/a
12	GABPA	chr15:78469722-78470080	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr15:78469731-78470031	SK-N-SH_RA	brain:	n/a	chr15:78469893-78469909
14	ZBTB7A	chr15:78469726-78470065	K562	blood:	n/a	n/a
15	CTCF	chr15:78469622-78470345	MCF-7	breast:	n/a	chr15:78469893-78469909
16	SMC3	chr15:78469621-78470210	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr15:78469622-78470230	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr15:78469720-78470108	H1-hESC	embryonic stem cell:	n/a	chr15:78469893-78469909
19	RAD21	chr15:78469632-78470232	H1-hESC	embryonic stem cell:	n/a	n/a
20	SMC3	chr15:78469719-78470099	K562	blood:	n/a	n/a
21	EP300	chr15:78469733-78469949	K562	blood:	n/a	n/a
22	CTCF	chr15:78469637-78470285	MCF-7	breast:	n/a	chr15:78469893-78469909
23	RAD21	chr15:78469500-78470445	SK-N-SH	brain:	n/a	n/a
24	RAD21	chr15:78469470-78470328	HCT-116	colon:	n/a	n/a
25	CTCF	chr15:78469186-78470715	A549	lung:	n/a	chr15:78469893-78469909
26	RAD21	chr15:78469657-78470218	A549	lung:	n/a	n/a
27	YY1	chr15:78469660-78470048	GM12878	blood:	n/a	chr15:78469901-78469910
28	RAD21	chr15:78469690-78470057	GM12878	blood:	n/a	n/a
29	RAD21	chr15:78469694-78470175	SK-N-SH_RA	brain:	n/a	n/a
30	MAX	chr15:78469719-78470380	MCF-7	breast:	n/a	n/a
31	RAD21	chr15:78469636-78470100	HepG2	liver:	n/a	n/a
32	RAD21	chr15:78469727-78470119	GM12878	blood:	n/a	n/a
33	CTCF	chr15:78469650-78470131	H1-hESC	embryonic stem cell:	n/a	chr15:78469893-78469909
34	CTCF	chr15:78469678-78470025	A549	lung:	n/a	chr15:78469893-78469909
35	CTCF	chr15:78469696-78470119	GM12878	blood:	n/a	chr15:78469893-78469909
36	CTCF	chr15:78469606-78470220	HCT-116	colon:	n/a	chr15:78469893-78469909
37	YY1	chr15:78469687-78470079	GM12878	blood:	n/a	chr15:78469901-78469910
38	CTCF	chr15:78469703-78470098	IMR90	lung:	n/a	chr15:78469893-78469909
39	RAD21	chr15:78469716-78470155	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr15:78469338-78470627	SK-N-SH	brain:	n/a	chr15:78469893-78469909
41	RAD21	chr15:78469617-78470251	MCF-7	breast:	n/a	n/a
42	CTCF	chr15:78469697-78470087	A549	lung:	n/a	chr15:78469893-78469909
43	RAD21	chr15:78469728-78470100	K562	blood:	n/a	n/a
44	SMC3	chr15:78469725-78470032	HepG2	liver:	n/a	n/a
45	YY1	chr15:78469637-78470181	H1-hESC	embryonic stem cell:	n/a	chr15:78469901-78469910
46	RAD21	chr15:78469634-78470107	HepG2	liver:	n/a	n/a
47	RAD21	chr15:78469684-78470117	H1-hESC	embryonic stem cell:	n/a	n/a
48	RAD21	chr15:78469617-78470142	ECC-1	luminal epithelium:	n/a	n/a
49	ZKSCAN1	chr15:78469740-78470015	Hela-S3	cervix:	n/a	n/a
50	RAD21	chr15:78469573-78470256	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78469399..78470392-chr15:78532758..78533807,5	K562	blood:
2	chr15:78469437..78470386-chr15:78487695..78488601,3	MCF-7	breast:
3	chr15:78469276..78470413-chr15:78534209..78535133,3	K562	blood:
4	chr15:78469629..78471471-chr15:78557003..78559345,2	MCF-7	breast:
5	chr15:78465044..78467906-chr15:78468275..78471070,3	K562	blood:
6	chr15:78469416..78470435-chr15:78487676..78488595,5	MCF-7	breast:
7	chr15:78439357..78441668-chr15:78468189..78471129,2	MCF-7	breast:
8	chr15:78469404..78471342-chr15:78532874..78534838,21	MCF-7	breast:
9	chr15:78405675..78406204-chr15:78469550..78470386,3	MCF-7	breast:
10	chr15:78469421..78470354-chr15:78532972..78533951,8	MCF-7	breast:
11	chr15:78423867..78424387-chr15:78469439..78470095,2	MCF-7	breast:

Variant related genes	Relation type
ACSBG1	TF binding region
ENSG00000166411	Chromatin interaction
ENSG00000136425	Chromatin interaction
ENSG00000103740	Chromatin interaction
ENSG00000140403	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11852636	0.84[ASN][1000 genomes]
rs12439537	0.87[ASN][1000 genomes]
rs12442037	0.84[ASN][1000 genomes]
rs12904700	0.82[ASN][1000 genomes]
rs16969548	0.87[ASN][1000 genomes]
rs2271901	0.84[ASN][1000 genomes]
rs2304823	0.98[ASN][1000 genomes]
rs2304825	0.82[ASN][1000 genomes]
rs3816253	0.82[ASN][1000 genomes]
rs56803002	0.99[ASN][1000 genomes]
rs74024174	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS 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	15 gene(s)	inside rSNPs	diseases
3	nsv904430	chr15:78466127-78507316	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78459000-78470000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:78460200-78474200	Weak transcription	HepG2	liver
4	chr15:78461800-78471000	Weak transcription	Psoas Muscle	Psoas
5	chr15:78464600-78469800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:78464800-78470000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:78464800-78475000	Weak transcription	HMEC	breast
8	chr15:78465000-78469800	Weak transcription	Hela-S3	cervix
9	chr15:78465000-78470000	Weak transcription	HSMM	muscle
10	chr15:78465200-78469800	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:78465200-78474200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:78465200-78475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:78465200-78475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:78465400-78470000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:78465400-78470000	Weak transcription	Placenta	Placenta
16	chr15:78465400-78474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:78465400-78475200	Weak transcription	NHEK	skin
18	chr15:78466000-78469800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:78466000-78469800	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:78466000-78470000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:78466200-78470000	Weak transcription	Left Ventricle	heart
22	chr15:78466400-78470200	Weak transcription	A549	lung
23	chr15:78466800-78469800	Weak transcription	Brain Anterior Caudate	brain
24	chr15:78466800-78473200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:78466800-78473400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:78467000-78469800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:78467000-78473200	Weak transcription	Aorta	Aorta
28	chr15:78467000-78473200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:78467000-78473400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:78467200-78477200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:78467400-78470000	Weak transcription	Brain Angular Gyrus	brain
32	chr15:78467400-78470000	Weak transcription	Brain Substantia Nigra	brain
33	chr15:78467400-78474800	Weak transcription	Fetal Brain Female	brain
34	chr15:78467400-78475400	Enhancers	Fetal Thymus	thymus
35	chr15:78467600-78469800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:78467600-78469800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:78467600-78472000	Weak transcription	Spleen	Spleen
38	chr15:78467800-78470000	Enhancers	Thymus	Thymus
39	chr15:78467800-78470800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:78468000-78469800	Weak transcription	Gastric	stomach
41	chr15:78468000-78469800	Weak transcription	GM12878-XiMat	blood
42	chr15:78468400-78471200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:78469400-78470000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:78469600-78470000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr15:78469600-78470600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr15:78469600-78470600	Enhancers	Right Ventricle	heart
47	chr15:78469600-78470600	Enhancers	HSMMtube	muscle

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