Variant report

Variant	rs180429
Chromosome Location	chr12:47177938-47177939
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12316767	0.85[GIH][hapmap]
rs1468970	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1468971	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1468972	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs180403	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs180405	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs180407	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs180408	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs180409	0.83[CHB][hapmap]
rs180410	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs180412	0.90[CHB][hapmap];0.82[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs180415	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs180416	0.91[CHB][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs180417	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs180419	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs180420	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs180421	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs180426	1.00[ASW][hapmap];0.80[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs180427	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs180428	0.81[ASN][1000 genomes]
rs180430	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080689	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2287471	0.85[GIH][hapmap]
rs2408623	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2430916	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2430920	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2430921	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2465582	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2465584	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2465595	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2465614	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2543334	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2543335	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2715775	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2715783	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7316285	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv826361	chr12:47159545-47200894	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs180429	SLC38A4	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47164200-47187800	Genic enhancers	Liver	Liver
2	chr12:47165200-47187200	Weak transcription	Fetal Kidney	kidney
3	chr12:47165600-47182000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:47168400-47180800	Weak transcription	Pancreas	Pancrea
5	chr12:47169400-47180000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:47169400-47182200	Weak transcription	Psoas Muscle	Psoas
7	chr12:47169400-47185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:47175200-47179200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:47175600-47178600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:47175600-47183000	Weak transcription	Aorta	Aorta
11	chr12:47177200-47178000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:47177200-47178200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:47177200-47178600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:47177200-47179000	Enhancers	HepG2	liver
15	chr12:47177200-47180800	Enhancers	Osteobl	bone
16	chr12:47177200-47181000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr12:47177400-47178000	Enhancers	Ovary	ovary
18	chr12:47177400-47181200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:47177400-47182400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:47177600-47180800	Enhancers	NHLF	lung
21	chr12:47177600-47181200	Enhancers	HSMM	muscle
22	chr12:47177800-47178600	Weak transcription	HSMMtube	muscle
23	chr12:47177800-47181000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr12:47177800-47182400	Enhancers	NHDF-Ad	bronchial

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