Variant report

Variant	rs11640405
Chromosome Location	chr16:79838311-79838312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10871380	0.95[ASN][1000 genomes]
rs11150199	0.90[ASN][1000 genomes]
rs11150200	0.92[ASN][1000 genomes]
rs11150201	0.96[ASN][1000 genomes]
rs11150202	0.97[ASN][1000 genomes]
rs11150203	0.97[ASN][1000 genomes]
rs11150204	0.97[ASN][1000 genomes]
rs11150205	0.98[ASN][1000 genomes]
rs11150206	0.98[ASN][1000 genomes]
rs11150207	0.98[ASN][1000 genomes]
rs11150208	0.98[ASN][1000 genomes]
rs11150209	0.98[ASN][1000 genomes]
rs11150210	0.94[ASN][1000 genomes]
rs11150211	0.98[ASN][1000 genomes]
rs11150212	0.98[ASN][1000 genomes]
rs11150213	0.98[ASN][1000 genomes]
rs11150214	0.97[ASN][1000 genomes]
rs11150215	0.97[ASN][1000 genomes]
rs11150216	0.97[ASN][1000 genomes]
rs11150219	0.96[ASN][1000 genomes]
rs11150220	0.92[ASN][1000 genomes]
rs1134715	0.95[ASN][1000 genomes]
rs11640419	0.97[ASN][1000 genomes]
rs11642817	0.96[ASN][1000 genomes]
rs11643810	0.93[ASN][1000 genomes]
rs11648556	0.88[ASN][1000 genomes]
rs11648855	0.97[ASN][1000 genomes]
rs11860693	0.97[ASN][1000 genomes]
rs11862561	0.90[ASN][1000 genomes]
rs11862593	0.90[ASN][1000 genomes]
rs11863874	0.97[ASN][1000 genomes]
rs11866244	0.96[ASN][1000 genomes]
rs12444097	0.91[ASN][1000 genomes]
rs12444100	0.89[ASN][1000 genomes]
rs12444123	0.92[ASN][1000 genomes]
rs12446125	0.90[ASN][1000 genomes]
rs12595956	0.98[ASN][1000 genomes]
rs12597506	0.98[ASN][1000 genomes]
rs12598926	0.88[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs12600157	0.88[ASN][1000 genomes]
rs12919529	0.89[ASN][1000 genomes]
rs12920397	0.97[ASN][1000 genomes]
rs12923698	0.89[ASN][1000 genomes]
rs12925344	0.89[ASN][1000 genomes]
rs12928764	0.96[ASN][1000 genomes]
rs12930441	0.97[ASN][1000 genomes]
rs12931444	0.94[ASN][1000 genomes]
rs12931584	0.94[ASN][1000 genomes]
rs12934885	0.92[ASN][1000 genomes]
rs3935177	0.92[ASN][1000 genomes]
rs4243184	0.94[ASN][1000 genomes]
rs4299168	0.97[ASN][1000 genomes]
rs4392086	0.97[ASN][1000 genomes]
rs4538028	0.97[ASN][1000 genomes]
rs4584830	0.94[ASN][1000 genomes]
rs4611477	0.92[ASN][1000 genomes]
rs4636922	0.92[ASN][1000 genomes]
rs4888047	0.88[ASN][1000 genomes]
rs4888048	0.95[ASN][1000 genomes]
rs4888049	0.95[ASN][1000 genomes]
rs4889029	0.89[ASN][1000 genomes]
rs4889030	0.89[ASN][1000 genomes]
rs4889031	0.92[ASN][1000 genomes]
rs4889032	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs4889033	0.95[ASN][1000 genomes]
rs4889034	0.97[ASN][1000 genomes]
rs4889035	0.97[ASN][1000 genomes]
rs6564706	0.97[ASN][1000 genomes]
rs7187906	0.97[ASN][1000 genomes]
rs7191989	0.97[ASN][1000 genomes]
rs8043824	0.96[ASN][1000 genomes]
rs8059641	0.93[ASN][1000 genomes]
rs9939031	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11640405	CHST6	cis	cerebellum	SCAN
rs11640405	SDR42E1	cis	cerebellum	SCAN
rs11640405	RP11-345M22.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79814000-79839600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:79831200-79839400	Weak transcription	Fetal Lung	lung
3	chr16:79834600-79838400	Weak transcription	K562	blood
4	chr16:79835400-79839600	Weak transcription	Thymus	Thymus
5	chr16:79836000-79838800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr16:79836200-79842400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr16:79838000-79838800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links