Variant report

Variant	rs1024120
Chromosome Location	chr4:28400119-28400120
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	chr4:28398298..28400403-chr4:28402842..28404450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250038	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10939211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722931	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11734656	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11735854	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12507595	0.91[ASN][1000 genomes]
rs12512541	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13111729	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13114507	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13116091	0.84[ASN][1000 genomes]
rs13139194	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13145217	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13145453	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1397439	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1510696	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1510700	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1705039	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17682996	0.91[ASN][1000 genomes]
rs1995910	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1995911	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2250259	0.82[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap]
rs4267724	0.84[ASN][1000 genomes]
rs4429724	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479514	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6448577	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664330	0.92[ASN][1000 genomes]
rs986866	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1005382	chr4:28157180-28403800	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	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
3	nsv1000514	chr4:28192982-28445194	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1012210	chr4:28246489-28419673	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1013013	chr4:28323465-28419673	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28390200-28404400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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