Variant report

Variant	rs13378425
Chromosome Location	chr13:48495021-48495022
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10220099	0.90[EUR][1000 genomes]
rs2406701	0.91[EUR][1000 genomes]
rs28628659	0.90[EUR][1000 genomes]
rs28794608	0.91[EUR][1000 genomes]
rs4496017	0.90[EUR][1000 genomes]
rs55845516	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6561423	0.87[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7317676	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7319779	0.91[EUR][1000 genomes]
rs840431	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs840434	0.87[CEU][hapmap]
rs9316341	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9591118	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9591119	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9591120	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9591121	0.87[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591122	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9591124	0.85[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9591125	0.91[EUR][1000 genomes]
rs9591126	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9591128	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9595805	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9595806	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9595808	0.90[AFR][1000 genomes]
rs9595809	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595810	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595811	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595814	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595816	1.00[EUR][1000 genomes]
rs9595819	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9595826	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9595827	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9595828	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9595830	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9595831	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9595832	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9595833	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1803690	chr13:48470681-48508091	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv3518029	chr13:48491634-48496241	Weak transcription ZNF genes & repeats Active TSS Enhancers	n/a	n/a	inside rSNPs	diseases
6	esv3518040	chr13:48491634-48496241	Weak transcription Enhancers ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13378425	SUCLA2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48477000-48506400	Weak transcription	Psoas Muscle	Psoas
2	chr13:48492200-48495400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:48492200-48510800	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links