Variant report

Variant	rs28376189
Chromosome Location	chr4:53430751-53430752
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	chr4:53430440..53432417-chr4:53577534..53579094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226950	Chromatin interaction
ENSG00000264585	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10000311	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10001085	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10001370	0.84[ASN][1000 genomes]
rs10001387	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10002261	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10010306	0.90[ASN][1000 genomes]
rs10012676	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10014752	0.90[ASN][1000 genomes]
rs10014850	0.84[ASN][1000 genomes]
rs10020568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021143	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10023867	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10027906	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10028085	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10028755	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10029145	0.90[ASN][1000 genomes]
rs10031386	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10032700	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10033218	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10471216	0.90[ASN][1000 genomes]
rs13434726	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13435157	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28376284	0.87[AFR][1000 genomes]
rs28379922	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28380682	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28396506	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402205	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28411005	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28412170	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28430452	0.90[ASN][1000 genomes]
rs28451750	0.90[ASN][1000 genomes]
rs28475600	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28478374	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28482298	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28503210	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28514875	0.87[AFR][1000 genomes]
rs28565016	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28588481	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28590396	0.90[ASN][1000 genomes]
rs28619184	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28644292	0.90[ASN][1000 genomes]
rs28651623	0.87[AFR][1000 genomes]
rs28654693	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28660550	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28660571	0.90[ASN][1000 genomes]
rs28672279	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28694544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28711292	0.87[AFR][1000 genomes]
rs28721897	0.90[ASN][1000 genomes]
rs28722174	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28784684	0.90[ASN][1000 genomes]
rs28825181	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs28825412	0.90[ASN][1000 genomes]
rs28849759	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28852068	0.90[ASN][1000 genomes]
rs6830833	0.90[ASN][1000 genomes]
rs7673679	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990686	0.90[ASN][1000 genomes]
rs9994643	0.90[ASN][1000 genomes]
rs9997863	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv999397	chr4:53157525-53448384	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv482581	chr4:53310749-53480710	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1009480	chr4:53338708-53436560	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv537092	chr4:53338708-53436560	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53421600-53434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:53427400-53431800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:53427400-53436200	Weak transcription	Right Ventricle	heart
4	chr4:53427600-53431800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:53427600-53432000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:53427600-53439000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:53427800-53432400	Weak transcription	HMEC	breast
8	chr4:53427800-53432400	Weak transcription	Osteobl	bone
9	chr4:53427800-53432800	Weak transcription	Fetal Heart	heart
10	chr4:53427800-53438800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:53430400-53433800	Weak transcription	H9 Cell Line	embryonic stem cell

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