Variant report

Variant	rs11181398
Chromosome Location	chr12:42666155-42666156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10459290	0.84[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10492388	0.92[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1051453	0.85[CEU][hapmap]
rs1059360	0.92[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10785333	0.92[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10785334	0.92[CEU][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880256	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10880258	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880259	0.93[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880260	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880261	0.89[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880264	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880268	0.92[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10880269	0.85[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880272	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10880273	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10880283	0.84[EUR][1000 genomes]
rs11181364	0.81[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181378	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11181380	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11181399	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181422	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11181454	0.80[EUR][1000 genomes]
rs11181463	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs11181465	0.80[EUR][1000 genomes]
rs11181466	0.80[EUR][1000 genomes]
rs11181467	0.80[EUR][1000 genomes]
rs11181483	0.80[EUR][1000 genomes]
rs11181499	0.80[EUR][1000 genomes]
rs12049942	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12228205	0.80[EUR][1000 genomes]
rs12308219	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366848	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12370778	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12371615	0.92[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12371762	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12815283	0.81[EUR][1000 genomes]
rs1551210	0.82[CEU][hapmap]
rs1669892	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1669936	0.80[EUR][1000 genomes]
rs17551006	0.89[CEU][hapmap]
rs1796380	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1796381	0.92[CEU][hapmap]
rs1796382	0.89[CEU][hapmap]
rs1796384	0.96[CEU][hapmap]
rs2178753	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2406567	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2406568	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2406674	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2708059	0.85[CEU][hapmap]
rs3747558	0.81[EUR][1000 genomes]
rs3747560	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs3810793	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4768399	0.89[CEU][hapmap]
rs4768402	0.80[EUR][1000 genomes]
rs4768411	0.88[CEU][hapmap]
rs56290913	0.81[EUR][1000 genomes]
rs6582390	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582391	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582395	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7138877	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71453350	0.81[EUR][1000 genomes]
rs7296357	0.81[EUR][1000 genomes]
rs7305397	0.89[CEU][hapmap]
rs7315968	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7957471	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7965392	0.80[EUR][1000 genomes]
rs7965743	0.80[EUR][1000 genomes]
rs7974476	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7974654	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9668610	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv826351	chr12:42584218-42676281	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv826352	chr12:42593124-42675255	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11181398	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs11181398	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42659600-42667800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:42662000-42667400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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