Variant report

Variant	rs12465380
Chromosome Location	chr2:40624522-40624523
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10182686	0.85[ASN][1000 genomes]
rs10201722	0.81[ASN][1000 genomes]
rs10208527	1.00[CHB][hapmap]
rs12478677	0.85[ASN][1000 genomes]
rs12611602	0.91[CHB][hapmap]
rs12611608	1.00[CHB][hapmap]
rs12712691	0.91[CHB][hapmap]
rs13405465	0.89[ASN][1000 genomes]
rs2041760	0.88[ASN][1000 genomes]
rs2041762	0.88[ASN][1000 genomes]
rs2041763	0.88[ASN][1000 genomes]
rs2041764	0.90[CHB][hapmap]
rs2192774	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2216008	0.84[ASN][1000 genomes]
rs2216009	0.82[GIH][hapmap]
rs34988656	0.88[ASN][1000 genomes]
rs4952410	0.83[CHB][hapmap]
rs56370629	0.80[ASN][1000 genomes]
rs57686441	0.85[ASN][1000 genomes]
rs6742210	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs7561383	1.00[CHB][hapmap];0.91[MEX][hapmap]
rs7581508	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs918001	0.83[CHB][hapmap]
rs994249	0.83[CHB][hapmap];0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873916	chr2:40607504-40649084	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12465380	GALM	cis	parietal	SCAN
rs12465380	ZFP36L2	cis	cerebellum	SCAN
rs12465380	EML4	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40619000-40624600	Weak transcription	Right Atrium	heart
2	chr2:40621200-40624800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr2:40622000-40625000	Enhancers	Colon Smooth Muscle	Colon
4	chr2:40622200-40635600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:40622600-40627600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:40622800-40624600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:40622800-40624800	Genic enhancers	Fetal Heart	heart
8	chr2:40622800-40626400	Weak transcription	Left Ventricle	heart
9	chr2:40622800-40627400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:40622800-40627400	Weak transcription	Brain Anterior Caudate	brain
11	chr2:40622800-40627400	Weak transcription	NH-A	brain
12	chr2:40622800-40627600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:40622800-40627600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:40622800-40627600	Weak transcription	Aorta	Aorta
15	chr2:40622800-40627600	Weak transcription	HSMMtube	muscle
16	chr2:40622800-40627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:40622800-40630400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:40622800-40630400	Weak transcription	Psoas Muscle	Psoas
19	chr2:40623000-40624600	Weak transcription	Fetal Brain Female	brain
20	chr2:40623000-40627200	Weak transcription	Adipose Nuclei	Adipose
21	chr2:40623000-40627400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:40623000-40627400	Weak transcription	HMEC	breast
23	chr2:40623000-40627400	Weak transcription	Osteobl	bone
24	chr2:40623000-40627600	Weak transcription	NHEK	skin
25	chr2:40623000-40627600	Weak transcription	NHLF	lung
26	chr2:40623000-40627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:40623000-40630400	Weak transcription	Fetal Brain Male	brain
28	chr2:40623000-40630800	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:40623000-40634800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:40623200-40627200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:40623200-40627600	Weak transcription	HSMM	muscle
32	chr2:40623400-40627200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:40623600-40627600	Weak transcription	Placenta	Placenta
34	chr2:40623600-40627600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:40623600-40627600	Weak transcription	NHDF-Ad	bronchial
36	chr2:40623600-40629800	Weak transcription	Brain Germinal Matrix	brain
37	chr2:40623600-40635000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:40623600-40655000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr2:40624200-40625400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:40624200-40633600	Weak transcription	Dnd41	blood
41	chr2:40624400-40625600	Enhancers	Right Ventricle	heart
42	chr2:40624400-40627600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:40624400-40627600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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