Variant report

Variant	rs4964413
Chromosome Location	chr12:106181544-106181545
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10507199	0.87[ASN][1000 genomes]
rs10732669	0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs10732670	0.89[ASN][1000 genomes]
rs10735409	0.87[ASN][1000 genomes]
rs10735410	0.91[ASN][1000 genomes]
rs10735411	0.86[ASN][1000 genomes]
rs10735412	0.85[ASN][1000 genomes]
rs10735413	0.85[ASN][1000 genomes]
rs10746050	0.84[ASN][1000 genomes]
rs10778440	0.86[ASN][1000 genomes]
rs10778441	0.89[ASN][1000 genomes]
rs10778442	0.89[ASN][1000 genomes]
rs10778446	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs10778447	0.85[ASN][1000 genomes]
rs10778448	0.88[ASN][1000 genomes]
rs10861505	0.87[ASN][1000 genomes]
rs10861511	0.81[ASN][1000 genomes]
rs10861512	0.87[ASN][1000 genomes]
rs10861513	0.85[ASN][1000 genomes]
rs10861514	0.94[ASN][1000 genomes]
rs10861515	0.94[ASN][1000 genomes]
rs10861517	0.85[ASN][1000 genomes]
rs11112724	0.87[ASN][1000 genomes]
rs11112729	0.89[ASN][1000 genomes]
rs11112730	0.90[ASN][1000 genomes]
rs11112731	0.87[ASN][1000 genomes]
rs11112733	0.89[ASN][1000 genomes]
rs11112736	0.87[ASN][1000 genomes]
rs11112737	0.89[ASN][1000 genomes]
rs11112739	0.94[ASN][1000 genomes]
rs11112747	0.88[ASN][1000 genomes]
rs11833529	0.87[ASN][1000 genomes]
rs12305658	0.87[ASN][1000 genomes]
rs12314159	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12370329	0.88[ASN][1000 genomes]
rs1421445	0.94[ASN][1000 genomes]
rs1421446	0.94[ASN][1000 genomes]
rs1421447	0.89[ASN][1000 genomes]
rs1477238	0.94[ASN][1000 genomes]
rs1477239	0.94[ASN][1000 genomes]
rs1477240	0.94[ASN][1000 genomes]
rs1477242	0.94[ASN][1000 genomes]
rs1549103	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2052428	0.89[ASN][1000 genomes]
rs2111975	0.91[ASN][1000 genomes]
rs2111976	0.91[ASN][1000 genomes]
rs2374538	0.94[ASN][1000 genomes]
rs2888869	0.87[ASN][1000 genomes]
rs4270016	0.85[ASN][1000 genomes]
rs4337138	0.85[ASN][1000 genomes]
rs4430602	0.94[ASN][1000 genomes]
rs4438139	0.89[ASN][1000 genomes]
rs4499093	0.87[ASN][1000 genomes]
rs4509865	0.89[ASN][1000 genomes]
rs4509866	0.95[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs4516058	0.93[ASN][1000 genomes]
rs4600310	0.87[ASN][1000 genomes]
rs4609683	0.83[ASN][1000 genomes]
rs4609684	0.87[ASN][1000 genomes]
rs4964160	0.93[ASN][1000 genomes]
rs4964161	0.93[ASN][1000 genomes]
rs4964409	0.87[ASN][1000 genomes]
rs4964410	0.89[ASN][1000 genomes]
rs4964411	0.95[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.89[ASN][1000 genomes]
rs4964414	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4964415	0.89[ASN][1000 genomes]
rs4964416	0.86[ASN][1000 genomes]
rs6539230	0.87[ASN][1000 genomes]
rs6539231	0.88[ASN][1000 genomes]
rs7302776	0.84[ASN][1000 genomes]
rs7303862	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7307825	0.93[ASN][1000 genomes]
rs7307959	0.91[ASN][1000 genomes]
rs7309925	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7311274	0.84[ASN][1000 genomes]
rs7313258	0.87[ASN][1000 genomes]
rs7313292	0.87[ASN][1000 genomes]
rs750207	0.89[ASN][1000 genomes]
rs750208	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7954139	0.93[ASN][1000 genomes]
rs7954308	0.93[ASN][1000 genomes]
rs7954604	0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs7956555	0.87[ASN][1000 genomes]
rs7964548	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7968050	0.88[ASN][1000 genomes]
rs7968132	0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7970318	0.87[ASN][1000 genomes]
rs7979193	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7979632	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs878612	0.87[ASN][1000 genomes]
rs9634186	0.89[ASN][1000 genomes]
rs9634187	0.88[ASN][1000 genomes]
rs9634188	0.88[ASN][1000 genomes]
rs9634189	0.89[ASN][1000 genomes]
rs9634227	0.95[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.89[ASN][1000 genomes]
rs9634228	0.95[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.89[ASN][1000 genomes]
rs9634229	0.89[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	nsv1039068	chr12:105935786-106211250	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1047810	chr12:106067049-106246582	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1040261	chr12:106068992-106246582	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv15321	chr12:106162101-106182216	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4964413	LHX9	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106178600-106182400	Weak transcription	Psoas Muscle	Psoas
2	chr12:106178800-106187400	Weak transcription	HSMMtube	muscle

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