Variant report

Variant	rs392469
Chromosome Location	chr5:8528618-8528619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTRR-4	chr5:8528589-8528785	NONHSAT100296

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10068072	0.83[ASN][1000 genomes]
rs1394642	0.95[ASN][1000 genomes]
rs16880714	0.97[ASN][1000 genomes]
rs16880716	0.95[ASN][1000 genomes]
rs16880725	0.95[ASN][1000 genomes]
rs16880754	0.98[ASN][1000 genomes]
rs2166872	0.95[ASN][1000 genomes]
rs365719	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368753	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371677	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372326	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs372588	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372695	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374142	0.98[ASN][1000 genomes]
rs374856	0.98[ASN][1000 genomes]
rs376041	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376478	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs377644	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377721	0.98[ASN][1000 genomes]
rs383026	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384423	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384797	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386120	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386332	0.98[ASN][1000 genomes]
rs391942	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393704	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394114	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394670	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs395753	0.98[ASN][1000 genomes]
rs396042	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs396055	0.98[ASN][1000 genomes]
rs397939	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398188	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398928	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402359	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404767	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414613	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418698	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432221	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs432665	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438193	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443746	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444945	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs446916	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449352	0.98[ASN][1000 genomes]
rs57085808	0.97[ASN][1000 genomes]
rs59216168	0.98[ASN][1000 genomes]
rs60932532	0.95[ASN][1000 genomes]
rs6870322	0.97[ASN][1000 genomes]
rs7718126	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033505	chr5:8258074-8657627	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv537634	chr5:8258074-8657627	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1026496	chr5:8275119-8681693	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
4	nsv537635	chr5:8275119-8681693	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
5	nsv880933	chr5:8467174-8688962	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv461929	chr5:8467900-8664747	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv597028	chr5:8467900-8664747	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv470987	chr5:8467900-8680327	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2755376	chr5:8504570-8547780	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv2756267	chr5:8504570-8547780	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv2756270	chr5:8504570-8547780	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1032346	chr5:8522331-8747061	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv537636	chr5:8522331-8747061	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv461930	chr5:8527086-8539813	Flanking Active TSS Active TSS Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases
15	nsv597029	chr5:8527086-8539813	Flanking Active TSS Weak transcription Enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs392469	SLC3A1	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:8517600-8532200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:8528400-8529800	Active TSS	Fetal Muscle Trunk	muscle
3	chr5:8528600-8528800	Flanking Active TSS	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links