Variant report

Variant	rs292071
Chromosome Location	chr4:28456089-28456090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10011519	0.83[AFR][1000 genomes]
rs1024120	0.82[CEU][hapmap]
rs10939211	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs13132764	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1510696	0.81[AMR][1000 genomes]
rs1510700	0.88[AMR][1000 genomes]
rs1705039	0.89[AMR][1000 genomes]
rs1708967	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs182378	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2250259	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2666117	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2666119	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs292026	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs292027	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs292031	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs292034	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs292066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs292068	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs292069	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs292070	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs292084	0.80[EUR][1000 genomes]
rs292085	0.80[EUR][1000 genomes]
rs4429724	0.84[AMR][1000 genomes]
rs481450	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55684803	0.80[EUR][1000 genomes]
rs567993	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs569100	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs569708	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs602888	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs604244	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6448577	0.88[AMR][1000 genomes]
rs666451	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs986866	0.88[AMR][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	nsv878775	chr4:28163856-28473048	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1010133	chr4:28273244-28642942	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1014938	chr4:28277683-28642942	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs292071	SLC34A2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28446000-28462400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:28446200-28464600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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