Variant report

Variant	rs13393247
Chromosome Location	chr2:114505406-114505407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:114503777..114505419-chr2:114513213..114515405,2	K562	blood:
2	chr2:114505270..114508161-chr2:114512124..114515717,3	K562	blood:
3	chr2:114502561..114504312-chr2:114505354..114506970,2	K562	blood:

Variant related genes	Relation type
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10169190	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197009	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199515	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208651	0.93[ASN][1000 genomes]
rs1062074	0.84[EUR][1000 genomes]
rs11123202	0.93[ASN][1000 genomes]
rs11123203	0.93[ASN][1000 genomes]
rs11677168	0.93[ASN][1000 genomes]
rs12329244	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711781	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711787	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12986781	0.86[ASN][1000 genomes]
rs13003858	0.86[ASN][1000 genomes]
rs13025042	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028979	0.93[ASN][1000 genomes]
rs13389017	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13395272	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401587	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407986	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13408264	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409879	0.81[EUR][1000 genomes]
rs13410586	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416738	0.87[EUR][1000 genomes]
rs13417896	0.93[ASN][1000 genomes]
rs13424899	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428433	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17048299	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17048506	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633451	0.87[EUR][1000 genomes]
rs28392566	0.84[EUR][1000 genomes]
rs34004564	0.81[EUR][1000 genomes]
rs34026450	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34451679	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34480436	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35049717	0.83[EUR][1000 genomes]
rs35073956	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35255260	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158991	0.81[ASN][1000 genomes]
rs62170066	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722177	0.87[ASN][1000 genomes]
rs7600251	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs998151	0.84[EUR][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	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13393247	ACTR3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:114461400-114513200	Weak transcription	Small Intestine	intestine
3	chr2:114465200-114512000	Weak transcription	Stomach Mucosa	stomach
4	chr2:114468800-114512800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:114469400-114510400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:114470200-114511200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:114470400-114510800	Strong transcription	HSMM	muscle
8	chr2:114474400-114507600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:114476000-114506600	Weak transcription	Thymus	Thymus
10	chr2:114478800-114507600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:114478800-114510600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:114479200-114510400	Strong transcription	Liver	Liver
13	chr2:114479800-114507000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:114481200-114513000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:114483000-114506600	Weak transcription	Psoas Muscle	Psoas
16	chr2:114484000-114511200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:114484400-114510600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:114484600-114512600	Weak transcription	Aorta	Aorta
19	chr2:114485200-114506400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:114485200-114511200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:114487200-114513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:114488400-114512600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:114492200-114513000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:114494200-114510400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr2:114494200-114510600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:114494200-114511000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:114494400-114509400	Strong transcription	Adipose Nuclei	Adipose
28	chr2:114494400-114511200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:114494400-114511600	Strong transcription	Osteobl	bone
30	chr2:114494600-114506000	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:114494600-114507000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:114494600-114510400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:114494800-114507200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr2:114494800-114510200	Strong transcription	HepG2	liver
35	chr2:114495000-114508800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:114495400-114509200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:114495800-114511200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:114495800-114512200	Weak transcription	Fetal Heart	heart
39	chr2:114496200-114505600	Strong transcription	NHLF	lung
40	chr2:114496200-114510600	Strong transcription	Placenta	Placenta
41	chr2:114496600-114510400	Strong transcription	NHDF-Ad	bronchial
42	chr2:114497400-114507200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:114497600-114510600	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:114498200-114506400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:114498400-114511400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:114499200-114506400	Weak transcription	Pancreas	Pancrea
47	chr2:114499200-114512600	Weak transcription	Esophagus	oesophagus
48	chr2:114499600-114506200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:114500000-114506000	Strong transcription	NHEK	skin
50	chr2:114500000-114507200	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links