Variant report

Variant	rs10490093
Chromosome Location	chr2:58925746-58925747
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	chr2:58923437..58926334-chr2:58929271..58931460,3	K562	blood:
2	chr2:58925351..58927966-chr7:107933916..107936194,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10490092	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13026438	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13421824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049642	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17190597	0.95[EUR][1000 genomes]
rs17190618	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17269154	0.98[EUR][1000 genomes]
rs17269182	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17549476	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17549656	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17549677	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17549712	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17549754	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17549803	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17550194	0.90[AMR][1000 genomes]
rs17550487	0.87[AMR][1000 genomes]
rs17614872	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17614895	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17615036	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615120	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615185	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615279	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615309	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615381	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615638	0.90[AMR][1000 genomes]
rs1922781	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1922783	0.90[AMR][1000 genomes]
rs1950160	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2204913	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35026255	0.82[AMR][1000 genomes]
rs55645922	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55745617	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174720	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56266136	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56365214	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60018257	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60888271	0.90[AMR][1000 genomes]
rs984881	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs984882	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs984883	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs993531	0.90[AMR][1000 genomes]
rs993532	0.90[AMR][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	nsv431180	chr2:58857542-59178687	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10490093	LOC339803	cis	parietal	SCAN
rs10490093	SPTBN1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58916800-58929200	Weak transcription	K562	blood
2	chr2:58925200-58925800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:58925200-58926600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:58925200-58926600	Enhancers	Fetal Brain Female	brain
5	chr2:58925200-58927000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:58925600-58926800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr2:58925600-58927000	Enhancers	Fetal Brain Male	brain

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