Variant report

Variant	rs10152127
Chromosome Location	chr15:56907855-56907856
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11071280	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11630168	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11636994	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11638707	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11852277	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11856558	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11857388	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11857706	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12148500	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438709	0.80[AMR][1000 genomes]
rs12442189	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12591502	0.87[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12592389	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12898521	0.89[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap]
rs12900244	0.89[CEU][hapmap];0.90[CHB][hapmap];0.96[JPT][hapmap]
rs12901887	0.86[CEU][hapmap]
rs12903283	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12903336	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903862	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12905514	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12908906	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910442	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12911191	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12911381	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12912666	0.84[CEU][hapmap]
rs12913361	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12916079	0.82[ASN][1000 genomes]
rs1424694	0.89[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap]
rs16977020	0.95[CHB][hapmap]
rs17238845	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979467	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1994081	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2170459	0.93[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2170463	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279298	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2279299	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28480089	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28620278	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3784554	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3803457	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3816752	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3929265	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4774244	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4774884	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4774886	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs538382	0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap]
rs553421	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs559736	0.80[AMR][1000 genomes]
rs7162317	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7165831	0.80[AMR][1000 genomes]
rs7168178	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes]
rs7169454	0.80[AMR][1000 genomes]
rs7174432	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7178796	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182187	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8025391	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes]
rs8043223	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1041239	chr15:56888945-56959028	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10152127	TCF12	cis	brain	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56902800-56945400	Weak transcription	Right Ventricle	heart
2	chr15:56905600-56923600	Weak transcription	Left Ventricle	heart
3	chr15:56907000-56912000	Weak transcription	Primary T cells from cord blood	blood
4	chr15:56907200-56908600	Enhancers	Dnd41	blood
5	chr15:56907800-56908800	Weak transcription	Fetal Thymus	thymus
6	chr15:56907800-56912000	Weak transcription	Thymus	Thymus

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