Variant report

Variant	rs2413787
Chromosome Location	chr15:45997434-45997435
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SQRDL-1	chr15:45997393-45997487	ENSG00000259200.1
2	lnc-SQRDL-1	chr15:45997276-45997487	ENSG00000259200.1

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10643	1.00[ASN][1000 genomes]
rs11629585	1.00[ASN][1000 genomes]
rs11634640	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2139647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56108595	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62006179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008310	1.00[ASN][1000 genomes]
rs62008318	1.00[ASN][1000 genomes]
rs62008319	1.00[ASN][1000 genomes]
rs62008320	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008321	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715101	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[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	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv523136	chr15:45990780-46158407	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45996000-45997800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr15:45996000-45998000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr15:45996000-45998000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:45996000-45998200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:45996200-45997800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:45996200-45998200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:45996200-45998200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr15:45996200-45998200	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr15:45996200-45998200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr15:45996400-45997600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:45996400-45997600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:45996400-45997600	Bivalent/Poised TSS	Fetal Brain Female	brain
13	chr15:45996400-45997600	Bivalent/Poised TSS	NH-A	brain
14	chr15:45996400-45997800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
15	chr15:45996400-45998000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr15:45996400-45998000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:45996400-45998000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:45996400-45998000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr15:45996400-45998000	Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr15:45996400-45998000	Active TSS	Brain Anterior Caudate	brain
21	chr15:45996400-45998000	Active TSS	Duodenum Mucosa	Duodenum
22	chr15:45996400-45998000	Active TSS	Rectal Smooth Muscle	rectum
23	chr15:45996400-45998200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:45996400-45998200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:45996400-45998200	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr15:45996400-45998200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:45996400-45998200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:45996400-45998200	Active TSS	Brain Angular Gyrus	brain
29	chr15:45996600-45997600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
30	chr15:45996600-45998000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:45996600-45998000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:45996600-45998000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:45996600-45998000	Active TSS	Aorta	Aorta
34	chr15:45996600-45998000	Active TSS	HSMM	muscle
35	chr15:45996600-45998000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
36	chr15:45996600-45998000	Active TSS	NHDF-Ad	bronchial
37	chr15:45996600-45998200	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr15:45996600-45998200	Active TSS	Brain Cingulate Gyrus	brain
39	chr15:45996600-45998200	Active TSS	Colon Smooth Muscle	Colon
40	chr15:45996600-45998200	Active TSS	NHEK	skin
41	chr15:45996600-45998400	Active TSS	Muscle Satellite Cultured Cells	--
42	chr15:45996800-45998000	Active TSS	Esophagus	oesophagus
43	chr15:45996800-45998000	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr15:45996800-45998000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
45	chr15:45996800-45998000	Active TSS	HepG2	liver
46	chr15:45996800-45998200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:45996800-45998200	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr15:45996800-45998200	Bivalent/Poised TSS	HSMMtube	muscle
49	chr15:45996800-45998200	Active TSS	Osteobl	bone
50	chr15:45997000-45997600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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