Variant report

Variant	rs28850298
Chromosome Location	chr4:143378744-143378745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143377636..143380466-chr4:143419571..143421151,2	MCF-7	breast:
2	chr4:143360196..143364725-chr4:143377583..143382490,5	MCF-7	breast:
3	chr4:143372548..143374141-chr4:143377111..143379331,2	MCF-7	breast:
4	chr4:143377586..143379612-chr4:143380437..143382675,2	MCF-7	breast:
5	chr4:143371682..143373996-chr4:143377086..143381453,3	MCF-7	breast:
6	chr4:143377913..143379697-chr4:143381987..143384286,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10012476	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10015184	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10015271	0.89[EUR][1000 genomes]
rs1013397	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12642500	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12643136	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12644565	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646243	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12649139	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1364917	0.80[AMR][1000 genomes]
rs1364918	0.80[AMR][1000 genomes]
rs1364919	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1364920	0.84[AMR][1000 genomes]
rs1364926	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1425534	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1425535	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1425538	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1603584	0.90[ASN][1000 genomes]
rs17016170	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17016195	0.91[EUR][1000 genomes]
rs17016207	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17016248	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17016284	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17016304	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2042644	0.86[AMR][1000 genomes]
rs2162108	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2322705	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2322706	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2322796	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28510314	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28823374	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28861843	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34900920	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3913164	0.91[EUR][1000 genomes]
rs3913165	0.91[EUR][1000 genomes]
rs4345256	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57724540	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59784151	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs60004938	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6823362	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7662794	0.91[EUR][1000 genomes]
rs7668133	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7672965	0.87[ASN][1000 genomes]
rs7695918	0.91[EUR][1000 genomes]
rs7699408	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9308152	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs931637	0.88[ASN][1000 genomes]
rs9986090	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9998089	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143367000-143392600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:143369200-143410600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:143371600-143400800	Weak transcription	Aorta	Aorta
4	chr4:143374200-143379800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:143377600-143381000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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