Variant report

Variant	rs71472930
Chromosome Location	chr15:52506549-52506550
allele	A/G
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	STAT3	chr15:52506527-52506662	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52505827..52511235-chr15:52516876..52519875,7	MCF-7	breast:

Variant related genes	Relation type
MYO5C	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1077383	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070882	0.86[AFR][1000 genomes]
rs11855672	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12593939	0.84[ASN][1000 genomes]
rs12595160	0.86[AFR][1000 genomes]
rs12903539	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12916135	0.80[ASN][1000 genomes]
rs34276836	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35712143	0.84[ASN][1000 genomes]
rs35827106	0.86[AFR][1000 genomes]
rs4774612	1.00[ASN][1000 genomes]
rs4776010	0.82[ASN][1000 genomes]
rs4776011	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4776013	0.82[ASN][1000 genomes]
rs4776014	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs66566761	0.84[ASN][1000 genomes]
rs66757864	0.81[EUR][1000 genomes]
rs67163040	0.84[ASN][1000 genomes]
rs67447954	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7164508	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7172037	0.84[ASN][1000 genomes]
rs7183278	0.82[ASN][1000 genomes]
rs8025737	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	nsv904220	chr15:52485024-52526507	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv1851383	chr15:52501831-52534344	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	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
8	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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52473200-52513600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52473600-52512400	Weak transcription	Primary B cells from cord blood	blood
3	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
4	chr15:52488600-52509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:52495600-52519000	Strong transcription	HepG2	liver
8	chr15:52497400-52509400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:52497400-52510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:52497400-52514600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:52497600-52508800	Weak transcription	Stomach Mucosa	stomach
13	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:52499000-52515600	Weak transcription	Left Ventricle	heart
15	chr15:52499200-52512600	Strong transcription	A549	lung
16	chr15:52500000-52512000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr15:52500000-52519000	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr15:52500600-52509200	Weak transcription	Brain Anterior Caudate	brain
19	chr15:52500800-52507400	Weak transcription	HUVEC	blood vessel
20	chr15:52501200-52506800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:52501400-52506800	Strong transcription	Pancreas	Pancrea
22	chr15:52501400-52512400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr15:52501600-52506800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr15:52501600-52519000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:52501600-52532600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:52501800-52506800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:52501800-52528000	Weak transcription	Fetal Heart	heart
28	chr15:52502000-52519200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:52502000-52523800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:52502400-52507000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:52502400-52520200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:52502600-52519000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:52502800-52506800	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr15:52502800-52506800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr15:52502800-52517800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:52503000-52506800	Strong transcription	Liver	Liver
37	chr15:52503000-52507000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:52503000-52507200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:52503200-52506800	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr15:52503200-52512400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr15:52503200-52519200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:52503800-52506800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:52504400-52512600	Weak transcription	Placenta	Placenta
44	chr15:52505000-52506800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:52505200-52506800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:52505200-52508200	Weak transcription	Fetal Intestine Small	intestine
47	chr15:52505400-52526800	Weak transcription	Right Ventricle	heart
48	chr15:52505600-52507000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr15:52505600-52507200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:52505600-52525600	Weak transcription	Brain Hippocampus Middle	brain

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