Variant report

Variant	rs10499084
Chromosome Location	chr6:118302310-118302311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10457323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10457324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10872160	0.82[EUR][1000 genomes]
rs10872161	0.82[EUR][1000 genomes]
rs11153710	0.93[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1160428	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11754631	0.83[JPT][hapmap]
rs12199369	0.85[EUR][1000 genomes]
rs12203409	0.82[AMR][1000 genomes]
rs12206792	0.94[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs12212649	0.89[EUR][1000 genomes]
rs12212953	0.86[EUR][1000 genomes]
rs12214395	0.80[EUR][1000 genomes]
rs1323100	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1323101	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1338968	0.84[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs1338974	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs1338975	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1416416	0.94[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1416417	0.93[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1416418	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1416419	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1416420	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1416421	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1416422	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1570447	0.94[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1980748	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1998458	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2139048	0.82[AMR][1000 genomes]
rs2211098	0.93[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs2355792	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2760240	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes]
rs2789010	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2789013	0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4946304	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4946305	0.82[ASN][1000 genomes]
rs6568991	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6903073	0.94[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6935283	0.81[ASN][1000 genomes]
rs6937496	0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7738597	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7775647	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs912088	0.88[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes]
rs9320623	0.85[GIH][hapmap]
rs9320624	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9372488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9374685	0.82[AMR][1000 genomes]
rs9374691	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9385024	0.80[AMR][1000 genomes]
rs9385027	0.94[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs9385028	0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs9387517	0.82[AMR][1000 genomes]
rs9387518	0.82[AMR][1000 genomes]
rs9387531	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9387535	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs9398465	0.82[AMR][1000 genomes]
rs9398468	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9401039	0.84[JPT][hapmap]
rs9401040	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9401044	1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9401046	0.93[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs9401051	0.86[CHB][hapmap]
rs9489295	0.94[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs982647	0.84[MEX][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	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10499084	LCK	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118296400-118305800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:118297200-118305600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links