Variant report

Variant	rs10174809
Chromosome Location	chr2:173386534-173386535
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	chr2:173384383..173387299-chr2:173419488..173421323,2	K562	blood:

Variant related genes	Relation type
ENSG00000152256	Chromatin interaction
ENSG00000225205	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12052479	1.00[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12465295	0.87[CHB][hapmap]
rs12465442	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs12467358	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs12469537	0.84[AFR][1000 genomes]
rs12474168	0.81[ASN][1000 genomes]
rs12474995	0.81[ASN][1000 genomes]
rs12477247	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs12478465	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs12619242	0.81[ASN][1000 genomes]
rs12622687	0.81[ASN][1000 genomes]
rs13383151	0.81[ASN][1000 genomes]
rs13398175	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs13402061	0.81[ASN][1000 genomes]
rs1574247	0.81[ASN][1000 genomes]
rs1574257	0.94[ASW][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16860543	0.86[CHB][hapmap]
rs2178474	0.81[ASN][1000 genomes]
rs2293646	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs2357415	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs34237921	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34871211	0.84[AFR][1000 genomes]
rs35022330	0.90[AFR][1000 genomes]
rs3792259	0.81[YRI][hapmap]
rs3792260	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs4075604	0.99[AFR][1000 genomes]
rs4308101	0.81[ASN][1000 genomes]
rs4972841	0.84[ASN][1000 genomes]
rs55966259	0.91[AFR][1000 genomes]
rs56832945	0.91[AFR][1000 genomes]
rs57957394	0.81[ASN][1000 genomes]
rs58016698	0.81[ASN][1000 genomes]
rs58044442	0.81[ASN][1000 genomes]
rs59610589	0.81[ASN][1000 genomes]
rs60446415	0.81[ASN][1000 genomes]
rs61194385	0.90[AFR][1000 genomes]
rs6718477	0.87[CHB][hapmap]
rs6730763	0.96[AFR][1000 genomes]
rs6755100	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs6759557	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs7562753	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7562865	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7565216	0.81[ASN][1000 genomes]
rs7591883	0.81[ASN][1000 genomes]
rs7596665	0.81[YRI][hapmap]

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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10174809	KLHL23	cis	parietal	SCAN
rs10174809	G6PC2	cis	cerebellum	SCAN
rs10174809	HOXD11	cis	parietal	SCAN
rs10174809	LOC91149	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173376400-173397400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:173383400-173386800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:173386000-173387400	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links