Variant report

Variant	rs9848979
Chromosome Location	chr3:118645118-118645119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11927719	0.89[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs12487299	0.83[EUR][1000 genomes]
rs12489856	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16829163	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs1879552	0.91[EUR][1000 genomes]
rs2110368	0.89[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs2110369	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2160052	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2215811	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2866317	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36052974	0.91[EUR][1000 genomes]
rs58464946	0.92[EUR][1000 genomes]
rs6765168	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6782002	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6786886	0.86[ASW][hapmap]
rs6795936	0.89[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs6802658	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73183699	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73185803	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7610212	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs9289117	0.86[ASW][hapmap]
rs9854506	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9878706	0.93[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9848979	IGSF11	cis	parietal	SCAN
rs9848979	IGSF11	cis	cerebellum	SCAN
rs9848979	B4GALT4	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118619800-118651400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:118620200-118663200	Weak transcription	Pancreas	Pancrea
3	chr3:118642200-118647000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:118642200-118647200	Weak transcription	Ovary	ovary
5	chr3:118642800-118645200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:118642800-118651400	Weak transcription	Brain Angular Gyrus	brain
7	chr3:118643200-118651600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:118643600-118647000	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:118643800-118645200	Enhancers	Brain Substantia Nigra	brain
10	chr3:118644600-118645400	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:118644600-118649000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:118645000-118645200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:118645000-118645400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr3:118645000-118645400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:118645000-118645600	Enhancers	Brain Anterior Caudate	brain
16	chr3:118645000-118646000	Enhancers	Brain Cingulate Gyrus	brain

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