Variant report

Variant	rs549042
Chromosome Location	chr10:97349134-97349135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10159941	0.92[CHB][hapmap]
rs10509687	1.00[CHB][hapmap]
rs10748634	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10748635	0.91[CHB][hapmap]
rs10748637	0.92[CHB][hapmap]
rs10748638	0.89[JPT][hapmap]
rs10748642	0.89[JPT][hapmap]
rs10748643	0.89[JPT][hapmap]
rs10786228	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs10786230	0.92[CHB][hapmap]
rs10786235	0.92[CHB][hapmap]
rs10882646	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10882651	0.84[JPT][hapmap]
rs10882652	0.84[JPT][hapmap]
rs10882653	0.92[CHB][hapmap]
rs10882656	0.89[JPT][hapmap]
rs10882657	0.89[JPT][hapmap]
rs10882660	0.89[JPT][hapmap]
rs10882664	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap]
rs11188414	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs11188459	0.92[CHB][hapmap]
rs11596004	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12244559	0.84[JPT][hapmap]
rs12262943	0.92[CHB][hapmap]
rs1418709	0.89[JPT][hapmap]
rs17111041	1.00[CHB][hapmap]
rs1890186	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1933165	0.89[JPT][hapmap]
rs1933166	0.92[CHB][hapmap]
rs1933169	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap]
rs1953710	0.92[CHB][hapmap]
rs2153913	0.89[JPT][hapmap]
rs2211002	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap]
rs2225893	1.00[CHB][hapmap]
rs2275273	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2297788	0.84[JPT][hapmap]
rs2485643	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2861147	0.89[JPT][hapmap]
rs2861148	0.87[JPT][hapmap]
rs2861149	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs3750700	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3750701	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3793748	1.00[CHB][hapmap]
rs3814159	0.89[JPT][hapmap]
rs3934409	0.89[JPT][hapmap]
rs3949478	0.85[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs4290159	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs4431963	0.89[JPT][hapmap]
rs4457685	0.92[CHB][hapmap]
rs4501930	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs4551688	0.89[JPT][hapmap]
rs4582902	0.89[JPT][hapmap]
rs479505	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4918950	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs4918962	0.89[JPT][hapmap]
rs4918964	0.92[CHB][hapmap]
rs496426	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs496641	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs497331	1.00[CHB][hapmap]
rs5014871	0.89[JPT][hapmap]
rs540145	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs540963	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs546138	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571505	1.00[CHB][hapmap]
rs6584022	0.89[JPT][hapmap]
rs6584023	0.89[JPT][hapmap]
rs6584026	0.92[CHB][hapmap]
rs6584027	0.89[JPT][hapmap]
rs7071836	0.89[JPT][hapmap]
rs7073723	0.92[CHB][hapmap]
rs7081414	0.92[CHB][hapmap]
rs7086986	0.89[JPT][hapmap]
rs7095587	0.89[JPT][hapmap]
rs7096317	0.84[JPT][hapmap]
rs7894648	0.84[JPT][hapmap]
rs7905653	0.92[CHB][hapmap]
rs7909569	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7918235	0.92[CHB][hapmap]
rs7920801	0.80[JPT][hapmap]
rs7920850	0.92[CHB][hapmap]
rs945958	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]

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	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs549042	ALDH18A1	cis	cerebellum	SCAN
rs549042	FRAT1	cis	cerebellum	SCAN
rs549042	ENTPD1	cis	lymphoblastoid	seeQTL
rs549042	C10orf12	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97335200-97373400	Weak transcription	Psoas Muscle	Psoas
2	chr10:97339600-97351400	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links