Variant report

Variant	rs17038091
Chromosome Location	chr12:106476402-106476403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10492351	0.82[JPT][hapmap]
rs1064959	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112866	0.81[AMR][1000 genomes]
rs12318540	0.82[JPT][hapmap]
rs1427793	0.82[JPT][hapmap]
rs1896364	0.82[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3741884	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3782692	0.81[AMR][1000 genomes]
rs73193841	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73193855	0.81[AMR][1000 genomes]
rs7485023	0.81[ASN][1000 genomes]
rs892270	1.00[JPT][hapmap]

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	nsv832509	chr12:106363888-106516221	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17038091	NUAK1	cis	cerebellum	SCAN
rs17038091	CKAP4	cis	cerebellum	SCAN
rs17038091	CKAP4	cis	parietal	SCAN
rs17038091	SLC41A2	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106458600-106476800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:106458800-106500200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:106461800-106499600	Weak transcription	Fetal Intestine Large	intestine
4	chr12:106462400-106482600	Weak transcription	Esophagus	oesophagus
5	chr12:106462600-106477400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:106462800-106477400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:106463800-106477600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:106464600-106477400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:106465200-106487000	Weak transcription	Brain Germinal Matrix	brain
10	chr12:106466200-106477600	Genic enhancers	HSMM	muscle
11	chr12:106467000-106477600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:106469000-106477400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:106469000-106490200	Weak transcription	Gastric	stomach
14	chr12:106469000-106499400	Weak transcription	Fetal Intestine Small	intestine
15	chr12:106469200-106477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:106471000-106477400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:106471200-106477400	Enhancers	Aorta	Aorta
18	chr12:106471400-106477600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:106471400-106478400	Enhancers	Right Atrium	heart
20	chr12:106471800-106476800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:106472000-106477400	Genic enhancers	NH-A	brain
22	chr12:106472000-106477600	Enhancers	NHLF	lung
23	chr12:106472000-106478400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:106472200-106477800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:106472200-106477800	Genic enhancers	A549	lung
26	chr12:106472200-106478000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:106472400-106478000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:106472400-106479400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:106472600-106476600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:106472600-106477000	Genic enhancers	HUVEC	blood vessel
31	chr12:106472600-106477600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:106472800-106480400	Weak transcription	Pancreas	Pancrea
33	chr12:106472800-106480600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:106473000-106476600	Weak transcription	HMEC	breast
35	chr12:106473000-106482000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:106473400-106477600	Strong transcription	Fetal Brain Female	brain
37	chr12:106473800-106477400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:106474000-106477400	Weak transcription	Fetal Kidney	kidney
39	chr12:106474600-106476600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr12:106474600-106477000	Enhancers	HepG2	liver
41	chr12:106474600-106477400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:106474600-106477400	Genic enhancers	Brain Hippocampus Middle	brain
43	chr12:106474600-106478000	Weak transcription	Fetal Lung	lung
44	chr12:106474600-106480000	Enhancers	NHDF-Ad	bronchial
45	chr12:106474600-106484600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:106474800-106477000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:106474800-106477400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr12:106474800-106478200	Strong transcription	Liver	Liver
49	chr12:106474800-106479800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:106475000-106477600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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