Variant report

Variant	rs10399673
Chromosome Location	chr1:47878626-47878627
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47871587..47874697-chr1:47877424..47879244,3	K562	blood:
2	chr1:47872841..47874697-chr1:47876449..47879170,2	K562	blood:
3	chr1:47874710..47877626-chr1:47877641..47879603,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225762	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10789507	0.81[JPT][hapmap]
rs11211508	0.81[JPT][hapmap]
rs11211513	0.81[JPT][hapmap]
rs11211517	0.85[JPT][hapmap]
rs12070024	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12090153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1316443	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2405922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472725	0.82[JPT][hapmap]
rs2622909	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2622917	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2622920	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622921	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622925	0.82[JPT][hapmap]
rs2742104	0.81[JPT][hapmap]
rs2758735	0.81[JPT][hapmap]
rs2820970	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2820971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2820974	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2821088	0.81[JPT][hapmap]
rs2821093	0.82[JPT][hapmap]
rs3088062	0.81[JPT][hapmap]
rs3125630	0.81[JPT][hapmap]
rs3125633	0.85[JPT][hapmap]
rs3125635	0.81[JPT][hapmap]
rs3125644	0.80[JPT][hapmap]
rs3738315	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3925058	0.81[JPT][hapmap]
rs4492666	0.81[JPT][hapmap]
rs4603175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55718554	0.94[EUR][1000 genomes]
rs571281	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6671254	0.81[JPT][hapmap]
rs6673882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6673934	0.92[EUR][1000 genomes]
rs6697248	0.81[JPT][hapmap]
rs7525650	0.82[JPT][hapmap]
rs7532148	0.81[JPT][hapmap]
rs7552140	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9436882	0.81[JPT][hapmap]
rs9436899	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10399673	CMPK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47873800-47879200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:47877400-47879000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:47878000-47879000	Enhancers	GM12878-XiMat	blood
4	chr1:47878000-47882000	Weak transcription	HSMM	muscle
5	chr1:47878600-47878800	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:47878600-47878800	Bivalent Enhancer	HepG2	liver

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