Variant report

Variant	rs885915
Chromosome Location	chr6:30202715-30202716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM26-2	chr6:30201166-30203164	ucscGeneNc_uc003npj_2

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1362089	0.87[ASN][1000 genomes]
rs1573295	0.93[ASN][1000 genomes]
rs2021366	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2074472	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2074473	0.85[ASN][1000 genomes]
rs2097772	0.89[ASN][1000 genomes]
rs2106070	0.91[ASN][1000 genomes]
rs2106071	0.87[ASN][1000 genomes]
rs2107196	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2158283	0.87[ASN][1000 genomes]
rs2253163	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2253164	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284164	0.89[ASN][1000 genomes]
rs2285801	0.88[ASN][1000 genomes]
rs2394737	0.86[ASN][1000 genomes]
rs2508029	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28441239	0.83[ASN][1000 genomes]
rs2844778	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2844782	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2844786	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3094131	0.93[ASN][1000 genomes]
rs3094132	0.93[ASN][1000 genomes]
rs3094139	0.97[ASN][1000 genomes]
rs3094140	0.93[ASN][1000 genomes]
rs3094614	0.91[ASN][1000 genomes]
rs3094615	0.88[ASN][1000 genomes]
rs3094637	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3094638	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3094639	0.84[ASN][1000 genomes]
rs3129694	0.89[ASN][1000 genomes]
rs3130381	0.91[ASN][1000 genomes]
rs3130382	0.91[ASN][1000 genomes]
rs3130383	0.91[ASN][1000 genomes]
rs3130384	0.91[ASN][1000 genomes]
rs3130386	0.91[ASN][1000 genomes]
rs3130387	0.89[ASN][1000 genomes]
rs3130388	0.93[ASN][1000 genomes]
rs3130389	0.97[ASN][1000 genomes]
rs3130391	0.93[ASN][1000 genomes]
rs3130393	0.92[ASN][1000 genomes]
rs3130394	0.93[ASN][1000 genomes]
rs3132665	0.91[ASN][1000 genomes]
rs3132668	0.92[ASN][1000 genomes]
rs3132669	0.91[ASN][1000 genomes]
rs3132671	0.91[ASN][1000 genomes]
rs3132672	0.91[ASN][1000 genomes]
rs3132673	0.98[ASN][1000 genomes]
rs3132674	0.98[ASN][1000 genomes]
rs35848695	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4959046	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6457164	0.86[ASN][1000 genomes]
rs6457165	0.86[ASN][1000 genomes]
rs6457167	0.86[ASN][1000 genomes]
rs718254	0.88[ASN][1000 genomes]
rs7382110	0.84[ASN][1000 genomes]
rs7383511	0.94[ASN][1000 genomes]
rs757257	0.90[ASN][1000 genomes]
rs765977	0.88[ASN][1000 genomes]
rs7763162	0.90[ASN][1000 genomes]
rs7764012	0.88[ASN][1000 genomes]
rs7774730	0.86[ASN][1000 genomes]
rs885914	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs916568	0.93[ASN][1000 genomes]
rs916571	0.97[ASN][1000 genomes]
rs916572	0.97[ASN][1000 genomes]
rs9261539	0.86[ASN][1000 genomes]
rs9261543	0.86[ASN][1000 genomes]
rs9261546	0.90[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	nsv884060	chr6:30190640-30203602	Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs885915	HLA-A	cis	lymphoblastoid	GTEx
rs885915	HIST1H2AM	cis	parietal	SCAN
rs885915	HIST1H2AI	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30201400-30203000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:30202600-30202800	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links