Variant report

Variant	rs28421709
Chromosome Location	chr15:58012896-58012897
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCOM1-1	chr15:58012493-58013126	ENSG00000261219.1

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11854253	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11854731	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11857147	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11858659	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16977648	0.86[EUR][1000 genomes]
rs7181032	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7181993	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7182316	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72745565	0.83[EUR][1000 genomes]
rs72745568	0.88[EUR][1000 genomes]
rs72745576	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72745583	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72745586	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72745594	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72747204	0.93[EUR][1000 genomes]
rs8034567	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv530682	chr15:57912502-58108285	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57999800-58014400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:57999800-58022400	Weak transcription	Esophagus	oesophagus
3	chr15:58000200-58015000	Weak transcription	Stomach Mucosa	stomach
4	chr15:58001400-58013000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:58005400-58014200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr15:58005400-58014400	Weak transcription	Brain Germinal Matrix	brain
7	chr15:58005400-58019200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:58005400-58020000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:58005800-58014200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:58006000-58014600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:58006200-58014200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr15:58006600-58013400	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:58006600-58020400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:58006800-58013600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:58006800-58013600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:58006800-58014000	Weak transcription	Pancreas	Pancrea
17	chr15:58006800-58014400	Weak transcription	Gastric	stomach
18	chr15:58006800-58014600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:58006800-58014800	Weak transcription	Spleen	Spleen
20	chr15:58006800-58017200	Weak transcription	Fetal Kidney	kidney
21	chr15:58006800-58017200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:58006800-58019000	Weak transcription	NHLF	lung
23	chr15:58006800-58025000	Weak transcription	Brain Angular Gyrus	brain
24	chr15:58006800-58029400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:58006800-58037800	Weak transcription	Aorta	Aorta
26	chr15:58007000-58013000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr15:58007000-58023600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:58007000-58024600	Weak transcription	Brain Substantia Nigra	brain
29	chr15:58007600-58014600	Weak transcription	Right Ventricle	heart
30	chr15:58007600-58017000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr15:58007600-58018400	Weak transcription	HMEC	breast
32	chr15:58007600-58025000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:58007600-58026800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:58007800-58014200	Weak transcription	Hela-S3	cervix
35	chr15:58007800-58014400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:58007800-58015400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr15:58007800-58015400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:58007800-58017800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:58007800-58018800	Weak transcription	NHEK	skin
40	chr15:58007800-58024600	Weak transcription	HUVEC	blood vessel
41	chr15:58007800-58025000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:58008600-58016200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:58009200-58013000	Strong transcription	Fetal Thymus	thymus
44	chr15:58009400-58013200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:58009800-58013000	Strong transcription	Liver	Liver
46	chr15:58009800-58013200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr15:58009800-58013200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr15:58009800-58013200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:58009800-58013400	Strong transcription	Primary T cells from cord blood	blood
50	chr15:58010000-58013000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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