Variant report

Variant	rs6539196
Chromosome Location	chr12:105653761-105653762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10778374	0.82[ASN][1000 genomes]
rs10778375	0.86[ASN][1000 genomes]
rs1109432	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112436	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1196750	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1196766	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1196767	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1196768	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1196776	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196778	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196779	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196781	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196785	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196788	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196804	0.83[EUR][1000 genomes]
rs1196809	0.83[EUR][1000 genomes]
rs1196814	0.83[EUR][1000 genomes]
rs1196822	0.82[EUR][1000 genomes]
rs1196835	0.82[EUR][1000 genomes]
rs1196836	0.82[EUR][1000 genomes]
rs1196854	0.84[EUR][1000 genomes]
rs1196856	0.85[EUR][1000 genomes]
rs1196860	0.82[EUR][1000 genomes]
rs1196866	0.85[EUR][1000 genomes]
rs1196867	0.83[EUR][1000 genomes]
rs1196868	0.85[EUR][1000 genomes]
rs1196878	0.82[EUR][1000 genomes]
rs1201657	0.85[EUR][1000 genomes]
rs1317941	0.87[ASN][1000 genomes]
rs17036869	0.85[ASN][1000 genomes]
rs1732378	0.85[EUR][1000 genomes]
rs1732379	0.85[EUR][1000 genomes]
rs2264066	0.84[EUR][1000 genomes]
rs2374448	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440708	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2440717	0.83[EUR][1000 genomes]
rs4964127	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4964346	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6539197	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs727888	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7309320	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310488	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969800	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]

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
rs6539196	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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