Variant report

Variant	rs9925462
Chromosome Location	chr16:72000195-72000196
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10492824	0.85[ASN][1000 genomes]
rs10492825	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10852509	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11645540	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs11647844	0.82[AFR][1000 genomes]
rs11647947	0.83[AFR][1000 genomes]
rs12149869	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12149877	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12444854	0.84[ASN][1000 genomes]
rs12445043	0.82[AFR][1000 genomes]
rs12445713	0.82[AFR][1000 genomes]
rs12448111	0.82[AFR][1000 genomes]
rs12708920	0.82[AFR][1000 genomes]
rs12708921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12708922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12919947	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12921355	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12925901	0.85[CHB][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs12926353	0.81[AFR][1000 genomes]
rs12926408	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12927381	0.82[AFR][1000 genomes]
rs12930036	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1549292	0.89[CHB][hapmap];0.85[GIH][hapmap]
rs16973500	0.89[CHB][hapmap];0.84[GIH][hapmap]
rs16973520	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303220	0.85[CHB][hapmap]
rs28629271	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28714527	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34150651	0.83[ASN][1000 genomes]
rs34235351	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34972708	0.86[ASN][1000 genomes]
rs35259348	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35338546	0.85[ASN][1000 genomes]
rs35800852	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499553	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66553600	0.81[ASN][1000 genomes]
rs7186518	0.81[AFR][1000 genomes]
rs7186712	0.82[AFR][1000 genomes]
rs8046159	0.82[AFR][1000 genomes]
rs8046703	0.82[AFR][1000 genomes]
rs8047643	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8051124	0.82[AFR][1000 genomes]
rs8051364	0.82[AFR][1000 genomes]
rs8053217	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8053861	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8053891	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8055242	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9928413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9930930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938025	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv572950	chr16:71988728-72020323	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9925462	HPR	cis	parietal	SCAN
rs9925462	HPR	cis	cerebellum	SCAN
rs9925462	ZFHX3	cis	parietal	SCAN
rs9925462	HP	cis	brain	seeQTL
rs9925462	SLC9A5	cis	cerebellum	SCAN
rs9925462	HP	cis	multi-tissue	Pritchard
rs9925462	HP	trans	brain	seeQTL
rs9925462	HPR	cis	brain	seeQTL
rs9925462	TXNL4B	cis	parietal	SCAN
rs9925462	NFATC3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71995800-72001000	Weak transcription	Brain Hippocampus Middle	brain
2	chr16:71996600-72000400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr16:71999600-72010600	Weak transcription	Liver	Liver
4	chr16:71999800-72003200	Weak transcription	HepG2	liver

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