Variant report

Variant	rs2619829
Chromosome Location	chr5:5518377-5518378
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:61)

rs_ID	r²[population]
rs10063885	0.87[CEU][hapmap]
rs1541799	0.85[TSI][hapmap]
rs2264076	0.95[ASN][1000 genomes]
rs252928	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs252929	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs252930	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs252934	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs252935	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs252937	0.82[ASN][1000 genomes]
rs252938	0.82[EUR][1000 genomes]
rs2560298	0.83[CEU][hapmap]
rs2560299	0.91[CEU][hapmap]
rs2560300	0.91[CEU][hapmap]
rs2578500	0.85[TSI][hapmap]
rs2578513	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2578514	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2578515	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2578516	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2578517	0.86[ASN][1000 genomes]
rs2578518	0.91[ASN][1000 genomes]
rs2578520	0.95[ASN][1000 genomes]
rs2578521	0.91[ASN][1000 genomes]
rs2578522	0.91[ASN][1000 genomes]
rs2578523	0.81[ASN][1000 genomes]
rs2578527	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2578529	0.83[ASN][1000 genomes]
rs2578552	0.87[TSI][hapmap]
rs2578553	0.91[CEU][hapmap];0.85[TSI][hapmap]
rs2578554	0.86[CEU][hapmap]
rs2578557	0.91[CEU][hapmap]
rs2578564	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs2578565	0.85[TSI][hapmap]
rs2591694	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2591696	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2591697	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591702	0.80[ASN][1000 genomes]
rs2591707	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2591708	0.91[ASN][1000 genomes]
rs2619830	0.91[ASN][1000 genomes]
rs2619831	0.91[ASN][1000 genomes]
rs2619832	0.91[ASN][1000 genomes]
rs2619833	0.91[ASN][1000 genomes]
rs2619834	0.83[ASN][1000 genomes]
rs2619855	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2652702	0.91[ASN][1000 genomes]
rs2652703	0.91[ASN][1000 genomes]
rs2652704	0.91[ASN][1000 genomes]
rs2652705	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2652706	0.95[ASN][1000 genomes]
rs2652707	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2652715	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2652726	0.91[ASN][1000 genomes]
rs2652727	0.90[ASN][1000 genomes]
rs2918251	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918260	0.86[CEU][hapmap]
rs2918261	0.82[TSI][hapmap]
rs2928223	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2928225	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3098377	0.87[CEU][hapmap];0.87[TSI][hapmap]
rs6894118	0.83[TSI][hapmap]
rs719080	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757981	chr5:5447098-5764620	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv2759319	chr5:5447098-5764620	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv596941	chr5:5511990-5636458	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv596942	chr5:5511990-5722063	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2619829	NDUFS6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5517200-5520400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:5517200-5521200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:5518000-5521200	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links