Variant report

Variant	rs17437979
Chromosome Location	chr5:107304101-107304102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10037490	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11739536	0.93[JPT][hapmap]
rs12054721	0.93[JPT][hapmap]
rs12651919	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655573	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12656140	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12657877	0.86[ASN][1000 genomes]
rs1433057	0.93[JPT][hapmap]
rs17437658	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17438307	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17439150	0.81[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2067765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28670811	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4582260	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55780614	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55958078	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58342334	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59711822	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73204759	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73204760	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73204762	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73204763	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73204764	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73204766	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73204790	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73204796	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73206507	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][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	nsv882682	chr5:107213361-107458336	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17437979	MAN2A1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107287400-107304600	Weak transcription	Aorta	Aorta
2	chr5:107287400-107308600	Weak transcription	Left Ventricle	heart
3	chr5:107295800-107305400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:107296200-107321000	Weak transcription	Primary T cells from cord blood	blood
5	chr5:107301000-107305200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:107302200-107310400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:107302400-107308400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:107302400-107309400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:107302400-107313800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:107302400-107334600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:107303000-107305800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:107303200-107309200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:107303400-107304200	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr5:107303600-107304600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr5:107303600-107306000	Enhancers	NHDF-Ad	bronchial
16	chr5:107303600-107306400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:107303800-107305000	Enhancers	NHLF	lung
18	chr5:107303800-107306000	Enhancers	Osteobl	bone
19	chr5:107303800-107306200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:107304000-107305000	Enhancers	HUVEC	blood vessel
21	chr5:107304000-107305400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:107304000-107305800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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