Variant report

Variant	rs56066716
Chromosome Location	chr15:52536475-52536476
allele	A/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	POLR2A	chr15:52536026-52536716	HL-60	blood:	n/a	n/a
2	SPI1	chr15:52536169-52536539	HL-60	blood:	n/a	chr15:52536226-52536235
3	SPI1	chr15:52535968-52536664	HL-60	blood:	n/a	chr15:52536226-52536235
4	POLR2A	chr15:52536015-52536690	HL-60	blood:	n/a	n/a
5	ELF1	chr15:52536436-52536657	K562	blood:	n/a	chr15:52536565-52536578
6	GABPA	chr15:52536006-52536781	HL-60	blood:	n/a	n/a
7	GABPA	chr15:52535847-52536934	HL-60	blood:	n/a	n/a
8	ZNF263	chr15:52536360-52536620	HEK293-T-REx	kidney:	n/a	n/a
9	REST	chr15:52536015-52536778	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52536445..52539563-chr15:52540903..52544563,5	K562	blood:
2	chr15:52531482..52533056-chr15:52536199..52538626,2	MCF-7	breast:

Variant related genes	Relation type
MYO5C	TF binding region

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17707007	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751610	0.86[EUR][1000 genomes]
rs41504447	0.98[ASN][1000 genomes]
rs4268699	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55676113	0.86[EUR][1000 genomes]
rs55712142	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55870025	1.00[ASN][1000 genomes]
rs62623565	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7168434	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1537	chr15:52502246-52537067	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:52505600-52549200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:52506400-52548800	Weak transcription	Fetal Kidney	kidney
4	chr15:52509400-52537200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:52514000-52539400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:52516000-52549400	Weak transcription	Left Ventricle	heart
7	chr15:52523400-52548600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
9	chr15:52525800-52554000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:52526000-52548800	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:52526200-52548200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:52527400-52548200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:52528000-52548800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:52528000-52548800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:52528200-52537000	Weak transcription	Thymus	Thymus
16	chr15:52528600-52542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:52528600-52549600	Weak transcription	Right Ventricle	heart
18	chr15:52530000-52537600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:52531600-52548600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr15:52532000-52549000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:52533200-52540000	Strong transcription	A549	lung
22	chr15:52533200-52540800	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:52533400-52542400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr15:52533600-52542200	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr15:52533800-52537200	Enhancers	Primary B cells from peripheral blood	blood
26	chr15:52533800-52538200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:52533800-52539600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:52533800-52539800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:52533800-52540000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr15:52533800-52541600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:52533800-52542000	Strong transcription	Gastric	stomach
32	chr15:52533800-52543200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr15:52533800-52543200	Strong transcription	HepG2	liver
34	chr15:52533800-52543600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:52533800-52543600	Strong transcription	Pancreas	Pancrea
36	chr15:52533800-52544400	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:52533800-52544400	Strong transcription	Fetal Intestine Small	intestine
38	chr15:52533800-52546000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:52533800-52548600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:52533800-52548800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr15:52534000-52536600	Strong transcription	Pancreatic Islets	Pancreatic Islet
42	chr15:52534000-52537200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:52534000-52538000	Strong transcription	Colonic Mucosa	Colon
44	chr15:52534000-52538400	Strong transcription	Fetal Intestine Large	intestine
45	chr15:52534000-52538800	Strong transcription	Adipose Nuclei	Adipose
46	chr15:52534000-52542400	Strong transcription	Fetal Stomach	stomach
47	chr15:52534200-52540200	Strong transcription	Liver	Liver
48	chr15:52534400-52543800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:52534400-52548200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:52534400-52548800	Weak transcription	Primary T cells from cord blood	blood

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