Variant report

Variant	rs60900225
Chromosome Location	chr12:39858660-39858661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39835363..39838062-chr12:39856075..39859606,4	MCF-7	breast:
2	chr12:39835374..39838989-chr12:39856195..39860050,4	K562	blood:
3	chr12:39851241..39854513-chr12:39858183..39861000,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10876972	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876989	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172108	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172120	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11172174	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172183	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172235	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172264	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172282	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172293	0.84[ASN][1000 genomes]
rs11172319	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172320	0.84[EUR][1000 genomes]
rs11172541	0.90[EUR][1000 genomes]
rs11172650	0.83[EUR][1000 genomes]
rs4378431	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4466883	0.84[EUR][1000 genomes]
rs4492858	0.87[ASN][1000 genomes]
rs4564382	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58240943	0.80[EUR][1000 genomes]
rs58613501	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59695906	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60263267	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6581188	0.90[EUR][1000 genomes]
rs73094410	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7962283	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7965222	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7966540	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7974928	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7979444	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1044049	chr12:39845078-39922808	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1051709	chr12:39846990-39899051	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv976606	chr12:39856893-39860999	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60900225	KIF21A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39854600-39858800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:39857200-39860800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr12:39858600-39858800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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