Variant report

Variant	rs11050423
Chromosome Location	chr12:29904312-29904313
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10843505	0.89[MEX][hapmap];0.92[AMR][1000 genomes]
rs11050425	0.90[JPT][hapmap]
rs11050426	0.85[GIH][hapmap];0.92[AMR][1000 genomes]
rs16934870	0.85[GIH][hapmap];0.92[AMR][1000 genomes]
rs60952280	0.92[AMR][1000 genomes]
rs73077434	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11050423	OVCH1	cis	parietal	SCAN
rs11050423	CCDC91	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29880000-29921200	Weak transcription	Fetal Kidney	kidney
2	chr12:29881600-29915800	Weak transcription	Brain Substantia Nigra	brain
3	chr12:29887400-29915600	Weak transcription	Brain Angular Gyrus	brain
4	chr12:29888800-29915600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:29890200-29915600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:29890600-29913000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:29892400-29904400	Weak transcription	Esophagus	oesophagus
8	chr12:29894600-29907200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:29894800-29904400	Weak transcription	Ovary	ovary
10	chr12:29895000-29910000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:29896200-29904400	Weak transcription	Lung	lung
12	chr12:29897200-29904400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:29897200-29905800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:29897200-29916000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:29897800-29905600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:29898000-29910000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:29898200-29915800	Weak transcription	Liver	Liver
18	chr12:29898600-29921200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:29900400-29907200	Strong transcription	Adipose Nuclei	Adipose
20	chr12:29900600-29908400	Strong transcription	Fetal Muscle Leg	muscle
21	chr12:29900800-29904600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr12:29901200-29907600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:29901200-29915800	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:29901600-29911600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:29902000-29906800	Strong transcription	Brain Anterior Caudate	brain
26	chr12:29902000-29908000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:29902200-29904400	Weak transcription	HSMM	muscle
28	chr12:29902200-29905400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:29902600-29905200	Weak transcription	HSMMtube	muscle
30	chr12:29902600-29915800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:29902800-29904600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
32	chr12:29903000-29904600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:29903000-29904600	Strong transcription	Spleen	Spleen
34	chr12:29903000-29904800	Strong transcription	Aorta	Aorta
35	chr12:29903000-29904800	Strong transcription	Fetal Stomach	stomach
36	chr12:29903000-29905200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr12:29903000-29906600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:29903000-29906800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:29903200-29904400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:29903200-29904600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:29903200-29904800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr12:29903200-29905000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr12:29903200-29905200	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:29903200-29906200	Weak transcription	Right Atrium	heart
45	chr12:29903200-29906400	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr12:29903200-29911000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:29903400-29904400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr12:29903400-29904400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:29903400-29904800	Strong transcription	Hela-S3	cervix
50	chr12:29903600-29904400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links