Variant report

Variant	rs348959
Chromosome Location	chr5:112820972-112820973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112817510..112822037-chr5:112849495..112852801,4	MCF-7	breast:
2	chr5:112819169..112822042-chr5:112827227..112829109,2	MCF-7	breast:
3	chr5:112811062..112815504-chr5:112818708..112822151,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1035408	0.85[AMR][1000 genomes]
rs1593953	0.84[AMR][1000 genomes]
rs164251	0.88[AMR][1000 genomes]
rs164253	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs171181	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs182987	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs190453	0.88[AMR][1000 genomes]
rs2416282	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2431548	0.90[AMR][1000 genomes]
rs2434664	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2434665	0.88[AMR][1000 genomes]
rs26983	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs27700	0.88[AMR][1000 genomes]
rs27718	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2914153	0.85[ASN][1000 genomes]
rs2914252	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348927	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348933	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs348949	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs348950	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs348953	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs368352	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs406288	0.89[AMR][1000 genomes]
rs423089	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs459428	0.90[AMR][1000 genomes]
rs461034	0.87[AMR][1000 genomes]
rs463216	0.89[AMR][1000 genomes]
rs465898	0.90[AMR][1000 genomes]
rs675353	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9686772	0.82[AMR][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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112807800-112821600	Weak transcription	HMEC	breast
2	chr5:112810200-112823000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:112810400-112821600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:112813400-112822800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:112820600-112821000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:112820600-112823000	Weak transcription	Right Ventricle	heart
7	chr5:112820800-112821000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:112820800-112821000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:112820800-112821000	Bivalent Enhancer	Thymus	Thymus

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