Variant report

Variant	rs28714362
Chromosome Location	chr15:57847697-57847698
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CGNL1-3	chr15:57846153-57847878	NONHSAT044077

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28417250	0.91[AFR][1000 genomes]
rs28480242	1.00[AFR][1000 genomes]
rs28489568	0.91[AFR][1000 genomes]
rs28609908	0.85[AFR][1000 genomes]
rs28611414	0.94[AFR][1000 genomes]
rs28671179	0.88[AFR][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	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57837800-57853000	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:57839800-57847800	Enhancers	Fetal Intestine Large	intestine
3	chr15:57840800-57848000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:57840800-57849400	Enhancers	Fetal Muscle Leg	muscle
5	chr15:57841000-57847800	Enhancers	Right Atrium	heart
6	chr15:57841000-57848000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr15:57841000-57848600	Enhancers	HSMMtube	muscle
8	chr15:57842000-57847800	Enhancers	Fetal Intestine Small	intestine
9	chr15:57842800-57848600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr15:57843000-57847800	Enhancers	Gastric	stomach
11	chr15:57843000-57848400	Enhancers	Placenta	Placenta
12	chr15:57843000-57848600	Enhancers	Fetal Lung	lung
13	chr15:57843400-57847800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:57844200-57848800	Enhancers	Fetal Heart	heart
15	chr15:57844600-57847800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr15:57844600-57852200	Weak transcription	HepG2	liver
17	chr15:57844600-57859000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:57844800-57848600	Enhancers	Hela-S3	cervix
19	chr15:57844800-57857400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:57845200-57847800	Enhancers	Brain Anterior Caudate	brain
21	chr15:57845200-57847800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr15:57845200-57852400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:57845200-57857600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:57845400-57848000	Enhancers	Brain Hippocampus Middle	brain
25	chr15:57845400-57848600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:57845800-57847800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:57845800-57847800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr15:57845800-57847800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr15:57846000-57847800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr15:57846000-57847800	Enhancers	Fetal Brain Female	brain
31	chr15:57846000-57848400	Enhancers	HSMM	muscle
32	chr15:57846200-57847800	Enhancers	Fetal Muscle Trunk	muscle
33	chr15:57846200-57847800	Enhancers	Fetal Stomach	stomach
34	chr15:57846200-57847800	Enhancers	Stomach Mucosa	stomach
35	chr15:57846200-57847800	Enhancers	Stomach Smooth Muscle	stomach
36	chr15:57846200-57852400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr15:57846400-57847800	Enhancers	Brain Substantia Nigra	brain
38	chr15:57846400-57848000	Enhancers	Fetal Kidney	kidney
39	chr15:57846400-57848200	Enhancers	NH-A	brain
40	chr15:57846400-57848400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr15:57846600-57847800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr15:57846600-57847800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:57846600-57847800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:57846600-57847800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr15:57846600-57847800	Enhancers	Ovary	ovary
46	chr15:57846800-57848400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:57846800-57861400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:57847000-57847800	Weak transcription	Fetal Brain Male	brain
49	chr15:57847000-57854600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr15:57847200-57847800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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