Variant report

Variant	rs4964346
Chromosome Location	chr12:105654362-105654363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105653802..105657280-chr12:105663370..105665652,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10778374	0.81[ASN][1000 genomes]
rs1109432	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11112436	0.83[EUR][1000 genomes]
rs1196750	0.85[EUR][1000 genomes]
rs1196758	0.95[CEU][hapmap]
rs1196766	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1196767	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196768	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1196776	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1196778	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1196779	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1196781	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1196785	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1196788	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1196796	1.00[CEU][hapmap]
rs1196804	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1196809	0.82[EUR][1000 genomes]
rs1196814	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1196822	0.81[EUR][1000 genomes]
rs1196835	0.81[EUR][1000 genomes]
rs1196836	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs1196838	1.00[CEU][hapmap]
rs1196854	0.84[EUR][1000 genomes]
rs1196856	0.84[EUR][1000 genomes]
rs1196860	0.81[EUR][1000 genomes]
rs1196866	0.84[EUR][1000 genomes]
rs1196867	0.83[EUR][1000 genomes]
rs1196868	0.84[EUR][1000 genomes]
rs1196878	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs1196882	0.87[CEU][hapmap]
rs1201657	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1317941	0.97[ASN][1000 genomes]
rs1732378	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1732379	0.84[EUR][1000 genomes]
rs2246510	0.95[CEU][hapmap]
rs2264066	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2374448	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2440708	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2440717	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4964127	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6539196	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6539197	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs727888	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7308195	0.81[CEU][hapmap]
rs7309320	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7310488	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7969800	0.98[AMR][1000 genomes];0.98[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
rs4964346	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105648200-105657400	Weak transcription	Esophagus	oesophagus
2	chr12:105652600-105657800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:105652600-105661400	Weak transcription	HSMMtube	muscle
4	chr12:105653200-105656000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:105653400-105661400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:105653400-105661400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:105653800-105655000	Weak transcription	NHDF-Ad	bronchial
8	chr12:105653800-105655400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:105654200-105654400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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