Variant report

Variant	rs10459239
Chromosome Location	chr12:51242403-51242404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10160844	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10459237	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10459238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs10747595	0.83[ASN][1000 genomes]
rs10747596	0.82[ASN][1000 genomes]
rs10747597	0.89[ASN][1000 genomes]
rs10747599	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783393	0.88[ASN][1000 genomes]
rs10783394	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10783395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783404	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10783405	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap]
rs10783406	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876099	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10876100	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs10876105	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876115	0.85[ASN][1000 genomes]
rs10876119	0.83[ASN][1000 genomes]
rs1096030	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1096031	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1103441	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169587	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169588	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11169589	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11169592	0.89[ASN][1000 genomes]
rs11169593	0.85[EUR][1000 genomes]
rs11169602	0.85[ASN][1000 genomes]
rs11169603	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169608	0.85[ASN][1000 genomes]
rs11169609	0.85[ASN][1000 genomes]
rs11169610	0.85[ASN][1000 genomes]
rs11169612	0.85[ASN][1000 genomes]
rs11169614	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11495280	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11533636	0.83[ASN][1000 genomes]
rs12578465	0.83[ASN][1000 genomes]
rs12578466	0.83[ASN][1000 genomes]
rs12581103	0.91[ASN][1000 genomes]
rs1362964	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1583697	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1631348	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1642997	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643004	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1659375	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2554852	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2554854	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2579077	0.95[CEU][hapmap]
rs3752667	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4483656	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768926	0.87[ASN][1000 genomes]
rs4768937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768938	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768939	0.91[ASN][1000 genomes]
rs73100855	0.88[ASN][1000 genomes]
rs7979616	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs829120	1.00[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs829122	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs829126	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829128	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829129	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs829132	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs829139	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829141	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829142	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829143	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs829144	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs844175	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860476	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv899078	chr12:51213433-51286750	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10459239	TUBA1B	cis	cerebellum	SCAN
rs10459239	KRT79	cis	cerebellum	SCAN
rs10459239	RHEBL1	cis	cerebellum	SCAN
rs10459239	LASS5	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51237000-51244400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:51237000-51244400	Weak transcription	Gastric	stomach
3	chr12:51237800-51246400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:51242000-51243400	Enhancers	Fetal Muscle Leg	muscle
5	chr12:51242200-51243000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr12:51242400-51242800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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