Variant report

Variant	rs28679378
Chromosome Location	chr15:52577028-52577029
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52576519..52579426-chr17:57922498..57924345,2	MCF-7	breast:
2	chr15:52562655..52564480-chr15:52574878..52577754,2	MCF-7	breast:
3	chr15:52536664..52559220-chr15:52576974..52590204,72	MCF-7	breast:
4	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:
5	chr15:52572320..52574802-chr15:52575555..52577846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17650694	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17650718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28776010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7161988	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162229	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7175545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7175663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73406657	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[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	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
4	esv3415688	chr15:52576160-52579658	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3440864	chr15:52576610-52579708	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
2	chr15:52550000-52579200	Weak transcription	Fetal Kidney	kidney
3	chr15:52554800-52582200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:52555000-52585000	Weak transcription	Left Ventricle	heart
5	chr15:52555200-52580600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:52556000-52587000	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:52558800-52579400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:52559400-52580600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:52561400-52580600	Weak transcription	Spleen	Spleen
10	chr15:52565800-52587000	Weak transcription	Right Atrium	heart
11	chr15:52568600-52579400	Weak transcription	Stomach Mucosa	stomach
12	chr15:52568800-52580000	Weak transcription	Colonic Mucosa	Colon
13	chr15:52570800-52580800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:52571200-52581000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:52571200-52585800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:52571200-52587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:52571400-52580600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:52571400-52580600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:52571600-52579200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr15:52571600-52579200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:52572200-52577600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:52572800-52579800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:52574000-52580200	Weak transcription	Right Ventricle	heart
24	chr15:52574400-52579200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:52574400-52580400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:52574600-52587000	Weak transcription	Brain Anterior Caudate	brain
27	chr15:52575000-52577400	Weak transcription	Fetal Intestine Large	intestine
28	chr15:52575000-52577800	Weak transcription	Gastric	stomach
29	chr15:52575000-52579400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:52575000-52585000	Weak transcription	Fetal Stomach	stomach
31	chr15:52575200-52577600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:52575200-52580600	Weak transcription	Adipose Nuclei	Adipose
33	chr15:52575400-52579200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:52575400-52579200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:52575400-52581000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:52575400-52582000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:52575800-52577600	Weak transcription	Fetal Intestine Small	intestine
38	chr15:52575800-52577800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:52575800-52579200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:52575800-52579200	Weak transcription	HepG2	liver
41	chr15:52575800-52579400	Weak transcription	Pancreas	Pancrea
42	chr15:52575800-52580400	Weak transcription	Esophagus	oesophagus
43	chr15:52575800-52580600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:52575800-52580800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:52576000-52579400	Weak transcription	Liver	Liver
46	chr15:52577000-52577400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
47	chr15:52577000-52578400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
48	chr15:52577000-52579000	Weak transcription	A549	lung
49	chr15:52577000-52579200	Weak transcription	Hela-S3	cervix

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