Variant report

Variant	rs2279608
Chromosome Location	chr15:57847842-57847843
allele	A/G
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: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11517	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11545026	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280364	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1690319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1690320	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1690321	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1690322	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16977582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs16977594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16977597	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1908193	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131732	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270487	0.89[AFR][1000 genomes]
rs2279609	1.00[ASN][1000 genomes]
rs2414514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641567	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28507301	0.87[ASN][1000 genomes]
rs2922229	1.00[CHB][hapmap]
rs2934424	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55924857	0.80[ASN][1000 genomes]
rs6493932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7181371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs74016268	0.80[ASN][1000 genomes]
rs74016270	0.80[ASN][1000 genomes]
rs74016271	0.80[ASN][1000 genomes]
rs9744909	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57837800-57853000	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:57840800-57848000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:57840800-57849400	Enhancers	Fetal Muscle Leg	muscle
4	chr15:57841000-57848000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr15:57841000-57848600	Enhancers	HSMMtube	muscle
6	chr15:57842800-57848600	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr15:57843000-57848400	Enhancers	Placenta	Placenta
8	chr15:57843000-57848600	Enhancers	Fetal Lung	lung
9	chr15:57844200-57848800	Enhancers	Fetal Heart	heart
10	chr15:57844600-57852200	Weak transcription	HepG2	liver
11	chr15:57844600-57859000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:57844800-57848600	Enhancers	Hela-S3	cervix
13	chr15:57844800-57857400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:57845200-57852400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:57845200-57857600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:57845400-57848000	Enhancers	Brain Hippocampus Middle	brain
17	chr15:57845400-57848600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:57846000-57848400	Enhancers	HSMM	muscle
19	chr15:57846200-57852400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:57846400-57848000	Enhancers	Fetal Kidney	kidney
21	chr15:57846400-57848200	Enhancers	NH-A	brain
22	chr15:57846400-57848400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr15:57846800-57848400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:57846800-57861400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:57847000-57854600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:57847200-57853400	Weak transcription	NHEK	skin
27	chr15:57847200-57854400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:57847400-57848600	Enhancers	Psoas Muscle	Psoas
29	chr15:57847400-57852200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:57847600-57849000	Enhancers	HUVEC	blood vessel
31	chr15:57847600-57851800	Weak transcription	Liver	Liver
32	chr15:57847600-57852200	Weak transcription	A549	lung
33	chr15:57847600-57852200	Weak transcription	HMEC	breast
34	chr15:57847600-57853400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:57847600-57854400	Weak transcription	Pancreas	Pancrea
36	chr15:57847600-57859200	Weak transcription	Right Ventricle	heart
37	chr15:57847800-57848200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr15:57847800-57848600	Weak transcription	Brain Anterior Caudate	brain
39	chr15:57847800-57850200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:57847800-57852000	Weak transcription	Stomach Mucosa	stomach
41	chr15:57847800-57852400	Weak transcription	Fetal Intestine Large	intestine
42	chr15:57847800-57852400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:57847800-57852600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:57847800-57853600	Weak transcription	Fetal Stomach	stomach
45	chr15:57847800-57859000	Weak transcription	Gastric	stomach
46	chr15:57847800-57859200	Weak transcription	Ovary	ovary
47	chr15:57847800-57859200	Weak transcription	Right Atrium	heart

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