Variant report

Variant	rs7024988
Chromosome Location	chr9:108616432-108616433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108612291..108614169-chr9:108614702..108617430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228948	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10122308	0.81[CHB][hapmap]
rs10739214	0.93[ASN][1000 genomes]
rs10759147	0.93[ASN][1000 genomes]
rs10816300	0.82[CHB][hapmap]
rs10816313	0.82[CHB][hapmap]
rs10816349	0.93[ASN][1000 genomes]
rs10816350	0.92[ASN][1000 genomes]
rs10978241	0.80[CHB][hapmap]
rs10978309	0.93[ASN][1000 genomes]
rs10978310	0.93[ASN][1000 genomes]
rs10978311	0.93[ASN][1000 genomes]
rs10978312	0.93[ASN][1000 genomes]
rs10978313	0.92[ASN][1000 genomes]
rs1806663	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1806664	0.91[ASN][1000 genomes]
rs2417646	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2417647	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28534814	0.96[ASN][1000 genomes]
rs2997726	0.89[ASN][1000 genomes]
rs2997727	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3010415	0.86[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3010964	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3105991	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7019053	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7030636	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs71501939	0.98[ASN][1000 genomes]
rs7854091	0.93[ASN][1000 genomes]
rs7854144	0.93[ASN][1000 genomes]
rs7862281	0.99[ASN][1000 genomes]
rs7865672	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs7869341	0.93[ASN][1000 genomes]
rs7869461	0.93[ASN][1000 genomes]
rs9299115	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1041073	chr9:108535813-108731343	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1036849	chr9:108582944-108651205	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1052684	chr9:108582944-108730280	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv615140	chr9:108592589-108725567	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv831679	chr9:108603112-108785347	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108613800-108619200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:108616000-108616800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:108616000-108618800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:108616400-108616800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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