Variant report

Variant	rs12816560
Chromosome Location	chr12:105653513-105653514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10778367	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs10861347	1.00[CHB][hapmap]
rs10861371	1.00[CHB][hapmap]
rs10861400	1.00[CHB][hapmap]
rs10861407	1.00[CHB][hapmap]
rs10861409	1.00[CHB][hapmap]
rs1107755	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107757	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112424	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112428	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11112434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112475	1.00[CHB][hapmap]
rs1196742	0.85[EUR][1000 genomes]
rs1196745	0.85[EUR][1000 genomes]
rs1196748	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1196749	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1196753	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs1196754	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs1196756	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1196760	1.00[CHB][hapmap]
rs1196764	0.85[EUR][1000 genomes]
rs1196765	0.86[EUR][1000 genomes]
rs1196770	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196772	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196780	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196782	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196786	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196787	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196789	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196790	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196791	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196793	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196795	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1196797	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196798	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196800	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1196801	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1196805	0.84[EUR][1000 genomes]
rs1196806	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1196807	0.84[EUR][1000 genomes]
rs1196808	0.83[EUR][1000 genomes]
rs1196811	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196813	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1196817	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1196818	1.00[CHB][hapmap]
rs1196819	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1196820	0.84[EUR][1000 genomes]
rs1196823	0.83[EUR][1000 genomes]
rs1196825	0.84[EUR][1000 genomes]
rs1196831	0.84[EUR][1000 genomes]
rs1196833	0.84[EUR][1000 genomes]
rs1196839	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1196841	0.84[EUR][1000 genomes]
rs1196842	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1196844	0.84[EUR][1000 genomes]
rs1196848	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1196851	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1196852	1.00[CHB][hapmap]
rs1196853	0.85[EUR][1000 genomes]
rs1196859	0.83[EUR][1000 genomes]
rs1196861	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1196862	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1196864	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1196869	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196871	0.82[EUR][1000 genomes]
rs1196872	0.83[EUR][1000 genomes]
rs1196873	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196874	0.84[EUR][1000 genomes]
rs1196881	1.00[CHB][hapmap]
rs1196884	0.83[CEU][hapmap]
rs1206559	0.84[EUR][1000 genomes]
rs1209308	0.81[CEU][hapmap]
rs1209637	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1211276	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1211277	0.84[EUR][1000 genomes]
rs1211626	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12369709	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12814458	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822081	1.00[CHB][hapmap]
rs1444610	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1621553	1.00[CHB][hapmap]
rs1663564	1.00[CHB][hapmap]
rs1663565	0.83[EUR][1000 genomes]
rs1732370	0.84[EUR][1000 genomes]
rs2257156	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2374449	0.85[CEU][hapmap]
rs2440715	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2440718	0.84[EUR][1000 genomes]
rs2464173	0.84[EUR][1000 genomes]
rs2464175	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs2464181	0.84[EUR][1000 genomes]
rs2464182	0.83[EUR][1000 genomes]
rs2888846	1.00[CHB][hapmap]
rs35679386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390426	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs4545651	1.00[CHB][hapmap]
rs4964331	0.85[CEU][hapmap]
rs6539183	0.85[CEU][hapmap]
rs67604711	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7132040	0.84[CEU][hapmap]
rs7132855	0.84[CEU][hapmap]
rs71441895	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299225	1.00[CHB][hapmap]
rs7302174	1.00[CHB][hapmap]
rs73181823	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959385	1.00[CHB][hapmap]
rs7963877	0.85[CEU][hapmap]
rs873119	0.95[EUR][1000 genomes]
rs935240	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs935241	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs935242	0.84[EUR][1000 genomes]
rs935244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935248	0.85[EUR][1000 genomes]
rs935249	0.84[EUR][1000 genomes]
rs9645791	1.00[CHB][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	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12816560	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105648200-105653800	Enhancers	NHDF-Ad	bronchial
2	chr12:105648200-105657400	Weak transcription	Esophagus	oesophagus
3	chr12:105651400-105653800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:105651800-105653800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:105652600-105657800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:105652600-105661400	Weak transcription	HSMMtube	muscle
7	chr12:105652800-105654200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:105653200-105656000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:105653400-105661400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:105653400-105661400	Weak transcription	Placenta Amnion	Placenta Amnion

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