Variant report

Variant	rs52824916
Chromosome Location	chr12:49993678-49993679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49992900-49993988	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49993213..49995668-chr12:49998189..50000775,3	K562	blood:
2	chr12:49960315..49962480-chr12:49993322..49995583,2	MCF-7	breast:
3	chr12:49991394..49993923-chr12:50016054..50019750,3	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNH3-1	chr12:49993609-49994926	ENSG00000250952
2	lnc-KCNH3-1	chr12:49993611-49993925	NONHSAT028118
3	lnc-FAM186B-2	chr12:49993252-49994917	NR_027450

No data

Variant related genes	Relation type
FAM186B	TF binding region
ENSG00000135436	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000187778	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10875964	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11169063	0.84[ASN][1000 genomes]
rs11169065	0.91[ASN][1000 genomes]
rs11169069	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169070	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11169073	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169076	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11169080	0.87[ASN][1000 genomes]
rs11169081	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169082	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169092	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11169097	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11169104	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11169106	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11169109	0.80[ASN][1000 genomes]
rs11169111	0.80[ASN][1000 genomes]
rs11169112	0.80[ASN][1000 genomes]
rs11169118	0.80[ASN][1000 genomes]
rs11169133	0.80[ASN][1000 genomes]
rs11833411	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11834380	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12296586	0.80[ASN][1000 genomes]
rs12299505	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12299513	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12303310	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12309940	0.81[AMR][1000 genomes]
rs12310510	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12311527	0.91[ASN][1000 genomes]
rs12311839	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12314795	0.80[ASN][1000 genomes]
rs12314878	0.97[ASN][1000 genomes]
rs12315224	0.80[ASN][1000 genomes]
rs12315791	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12317646	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12320556	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12321819	0.97[ASN][1000 genomes]
rs13066	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13906	0.97[ASN][1000 genomes]
rs1470906	0.80[ASN][1000 genomes]
rs1574326	0.80[ASN][1000 genomes]
rs17123808	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1902329	0.91[ASN][1000 genomes]
rs1902330	0.91[ASN][1000 genomes]
rs2005195	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241418	0.97[ASN][1000 genomes]
rs2278068	0.97[ASN][1000 genomes]
rs2278069	0.97[ASN][1000 genomes]
rs2278070	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303305	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336058	0.80[ASN][1000 genomes]
rs2878532	0.81[ASN][1000 genomes]
rs3815832	0.97[ASN][1000 genomes]
rs3887727	0.87[ASN][1000 genomes]
rs3887728	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4045193	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4073998	0.84[ASN][1000 genomes]
rs4133070	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4563	0.80[ASN][1000 genomes]
rs4584654	0.80[ASN][1000 genomes]
rs55853522	0.97[ASN][1000 genomes]
rs57191490	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57342147	0.80[ASN][1000 genomes]
rs57916875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58278271	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59940006	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60121503	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61512987	0.81[ASN][1000 genomes]
rs61620972	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61710637	0.80[ASN][1000 genomes]
rs6580719	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7131915	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132792	0.91[ASN][1000 genomes]
rs7136052	0.80[ASN][1000 genomes]
rs7137976	0.80[ASN][1000 genomes]
rs7296281	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7299002	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7301209	0.97[ASN][1000 genomes]
rs7313738	0.80[ASN][1000 genomes]
rs73305008	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73305012	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73305085	0.85[AMR][1000 genomes]
rs73305098	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs73306808	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs74089182	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7952734	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7952938	0.84[ASN][1000 genomes]
rs7953911	0.97[ASN][1000 genomes]
rs7954994	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7956089	0.80[ASN][1000 genomes]
rs7956181	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7962645	0.80[ASN][1000 genomes]
rs7965658	0.94[ASN][1000 genomes]
rs7970241	0.97[ASN][1000 genomes]
rs7973389	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7975599	0.97[ASN][1000 genomes]
rs7977389	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7979262	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7979285	0.87[ASN][1000 genomes]
rs7980979	0.80[ASN][1000 genomes]
rs8626	0.81[ASN][1000 genomes]
rs876889	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs933738	0.92[ASN][1000 genomes]
rs9804749	0.80[ASN][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	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS 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	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49963000-50003200	Weak transcription	Aorta	Aorta
2	chr12:49976800-49994000	Weak transcription	Liver	Liver
3	chr12:49977600-49996200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:49978800-49994600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:49979600-50002600	Weak transcription	HepG2	liver
6	chr12:49979800-49995600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:49979800-49998800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:49980400-50000200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:49981000-49994000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:49982200-49993800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:49982600-50015400	Weak transcription	Pancreas	Pancrea
12	chr12:49982800-49994000	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:49982800-49996000	Weak transcription	Brain Angular Gyrus	brain
14	chr12:49983000-49996000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:49983200-49994000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:49983200-49994000	Weak transcription	Adipose Nuclei	Adipose
17	chr12:49983200-49994400	Weak transcription	Right Ventricle	heart
18	chr12:49983200-49995000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:49983200-49999400	Weak transcription	HSMMtube	muscle
20	chr12:49983200-50002800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:49983400-49994800	Weak transcription	HSMM	muscle
22	chr12:49983400-50002800	Weak transcription	NHEK	skin
23	chr12:49985000-49994800	Weak transcription	Ovary	ovary
24	chr12:49985200-49998600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:49985200-49998600	Weak transcription	Placenta	Placenta
26	chr12:49985200-50003000	Weak transcription	Lung	lung
27	chr12:49985400-49993800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:49985400-49996200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:49985400-49997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:49985400-49998000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:49985600-49993800	Weak transcription	Primary T cells from cord blood	blood
32	chr12:49985600-49993800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:49985600-49994000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:49985600-49995800	Weak transcription	Thymus	Thymus
35	chr12:49985600-49998800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:49985800-49998400	Weak transcription	Fetal Lung	lung
37	chr12:49987200-49998600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:49990600-49998400	Weak transcription	Fetal Heart	heart
39	chr12:49991800-49996800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:49992000-49995000	Strong transcription	Fetal Stomach	stomach
41	chr12:49992200-49995200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr12:49992800-49995000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:49992800-49996000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:49992800-50003200	Weak transcription	Fetal Intestine Large	intestine
45	chr12:49993000-49994400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:49993000-49995200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:49993200-49994000	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:49993200-49995000	Strong transcription	Fetal Intestine Small	intestine
49	chr12:49993200-49995400	Strong transcription	Fetal Muscle Leg	muscle
50	chr12:49993400-49994400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

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