Variant report

Variant	rs16827747
Chromosome Location	chr3:157221966-157221967
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12494755	0.83[EUR][1000 genomes]
rs12494965	0.95[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12496305	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12634385	0.95[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12634412	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1350149	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1378801	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16827688	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2165873	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2316337	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2316348	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34316188	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4679797	0.95[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4680369	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4680371	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4680372	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62278653	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62278654	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62278655	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62280977	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62280978	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62280979	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62280980	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62280981	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6441133	0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67228252	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6795972	0.84[EUR][1000 genomes]
rs73158530	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9682174	0.95[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16827747	C3orf33	cis	parietal	SCAN
rs16827747	VEPH1	cis	cerebellum	SCAN
rs16827747	C3orf55	cis	parietal	SCAN
rs16827747	RAD9A	trans	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157217400-157222200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:157217800-157235400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:157218800-157222200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:157219000-157222000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:157220000-157222200	Weak transcription	HUVEC	blood vessel
6	chr3:157220600-157222000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr3:157220800-157222000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:157220800-157222000	Enhancers	HSMMtube	muscle
9	chr3:157220800-157222600	Enhancers	HSMM	muscle
10	chr3:157221200-157222200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:157221200-157222200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:157221200-157222200	Weak transcription	Pancreas	Pancrea
13	chr3:157221400-157222000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:157221400-157222000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:157221400-157222600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:157221600-157222000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:157221600-157222400	Weak transcription	Fetal Kidney	kidney
18	chr3:157221600-157222600	Enhancers	Brain Germinal Matrix	brain
19	chr3:157221800-157226000	Weak transcription	Osteobl	bone
20	chr3:157221800-157244800	Weak transcription	NH-A	brain

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