Variant report

Variant	rs4964127
Chromosome Location	chr12:105646395-105646396
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105629810..105631890-chr12:105644832..105647203,2	MCF-7	breast:
2	chr12:105628268..105630407-chr12:105646094..105648967,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10778371	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1109432	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11112436	0.82[EUR][1000 genomes]
rs1196750	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1196766	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1196767	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1196768	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196776	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196778	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196779	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1196781	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1196785	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1196788	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196804	0.84[EUR][1000 genomes]
rs1196809	0.84[EUR][1000 genomes]
rs1196814	0.84[EUR][1000 genomes]
rs1196822	0.83[EUR][1000 genomes]
rs1196835	0.83[EUR][1000 genomes]
rs1196836	0.83[EUR][1000 genomes]
rs1196838	0.80[EUR][1000 genomes]
rs1196854	0.85[EUR][1000 genomes]
rs1196856	0.86[EUR][1000 genomes]
rs1196860	0.83[EUR][1000 genomes]
rs1196866	0.86[EUR][1000 genomes]
rs1196867	0.84[EUR][1000 genomes]
rs1196868	0.86[EUR][1000 genomes]
rs1196878	0.83[EUR][1000 genomes]
rs1201657	0.86[EUR][1000 genomes]
rs1732378	0.86[EUR][1000 genomes]
rs1732379	0.86[EUR][1000 genomes]
rs2264066	0.85[EUR][1000 genomes]
rs2374448	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2440708	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2440717	0.84[EUR][1000 genomes]
rs4964344	0.88[ASN][1000 genomes]
rs4964345	0.88[ASN][1000 genomes]
rs4964346	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6539196	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6539197	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs727888	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7300300	0.88[ASN][1000 genomes]
rs7309320	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7310488	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7969800	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7974354	0.85[ASN][1000 genomes]
rs7974694	0.84[ASN][1000 genomes]
rs7978648	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
2	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	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
rs4964127	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105645800-105646400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:105645800-105648200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr12:105646000-105646600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:105646200-105646400	Enhancers	Aorta	Aorta
5	chr12:105646200-105647400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:105646200-105647800	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links