Variant report

Variant	rs13088816
Chromosome Location	chr3:53894968-53894969
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACTR8-1	chr3:53893020-53895603	NONHSAT090006
2	lnc-ACTR8-1	chr3:53893021-53895603	ENSG00000271976.1

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13071560	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13073855	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13096326	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2232338	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2232341	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34310576	0.85[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34431816	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34443284	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34549821	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34938855	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35222185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36102758	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62619200	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66535155	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66583280	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66720724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66818866	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67340660	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71617207	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53881200-53895000	Weak transcription	A549	lung
2	chr3:53881200-53895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:53884000-53895800	Strong transcription	HepG2	liver
4	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
5	chr3:53885400-53895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:53885600-53896600	Weak transcription	Right Ventricle	heart
7	chr3:53886200-53897200	Weak transcription	Colonic Mucosa	Colon
8	chr3:53887800-53898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
10	chr3:53889000-53901400	Weak transcription	Esophagus	oesophagus
11	chr3:53889600-53895200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:53889600-53896000	Strong transcription	Pancreas	Pancrea
13	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:53889800-53895400	Weak transcription	NHDF-Ad	bronchial
15	chr3:53890000-53895800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:53890000-53904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:53890200-53895800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:53890400-53895200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:53890400-53898600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:53890400-53898800	Weak transcription	NH-A	brain
21	chr3:53890400-53903600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:53891000-53895000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:53891000-53895800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:53891000-53898000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:53891000-53898000	Weak transcription	Spleen	Spleen
27	chr3:53891000-53914200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:53891000-53914200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr3:53891200-53895000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:53891200-53897800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:53891200-53898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:53891200-53900800	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:53891200-53910800	Strong transcription	Fetal Stomach	stomach
34	chr3:53891400-53898400	Weak transcription	Small Intestine	intestine
35	chr3:53891400-53914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:53891600-53895000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:53891600-53895000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:53891600-53897800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:53891600-53904000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:53891800-53895200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr3:53891800-53912800	Strong transcription	Brain Germinal Matrix	brain
42	chr3:53892000-53895000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr3:53892000-53914400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:53892200-53895000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:53892200-53897000	Strong transcription	Fetal Intestine Large	intestine
46	chr3:53892200-53912400	Strong transcription	Fetal Brain Female	brain
47	chr3:53892200-53914000	Strong transcription	Adipose Nuclei	Adipose
48	chr3:53892200-53914400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:53892200-53914600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:53892400-53899400	Strong transcription	H1 Cell Line	embryonic stem cell

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