Variant report

Variant	rs71644709
Chromosome Location	chr1:223019840-223019841
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10495202	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1132369	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1132371	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11588378	0.90[EUR][1000 genomes]
rs12734196	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17475753	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17475774	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17476063	0.82[ASN][1000 genomes]
rs17477752	0.83[EUR][1000 genomes]
rs17534704	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17534774	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17535004	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17535032	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17535137	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17536056	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17536209	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17536299	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17536396	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17536522	0.83[EUR][1000 genomes]
rs34080450	0.90[EUR][1000 genomes]
rs34151467	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34194482	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34225287	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34277924	0.83[EUR][1000 genomes]
rs34299243	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34355153	0.90[EUR][1000 genomes]
rs34503525	0.90[EUR][1000 genomes]
rs34643369	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34690779	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34713681	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34755094	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34761499	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34774807	0.90[EUR][1000 genomes]
rs34791822	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34804073	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34893395	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34962524	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35131473	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35197173	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35217299	0.90[EUR][1000 genomes]
rs35270996	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35283922	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35319605	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35356885	0.83[EUR][1000 genomes]
rs35399857	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35506390	0.90[EUR][1000 genomes]
rs35538644	0.90[EUR][1000 genomes]
rs35551242	0.86[EUR][1000 genomes]
rs35578837	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35597626	0.90[EUR][1000 genomes]
rs35597790	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35689138	0.90[EUR][1000 genomes]
rs35756512	0.83[EUR][1000 genomes]
rs35773347	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35898924	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35912520	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35947021	0.87[EUR][1000 genomes]
rs36032255	0.83[EUR][1000 genomes]
rs36066427	0.83[EUR][1000 genomes]
rs36090356	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36113407	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4298738	0.90[EUR][1000 genomes]
rs61838118	0.83[EUR][1000 genomes]
rs61838119	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61839587	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61839588	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61839600	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61839601	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61839602	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61840263	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61840271	0.90[EUR][1000 genomes]
rs61840273	0.90[EUR][1000 genomes]
rs71644708	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71644714	0.90[EUR][1000 genomes]
rs71644716	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71644718	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1833087	chr1:223017325-223023604	Active TSS Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	esv1840619	chr1:223017325-223023604	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
7	esv1840763	chr1:223017325-223023604	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv442589	chr1:223017325-223023604	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs71644709	RP11-452F19.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222989400-223026800	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:222990400-223027400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:223010800-223027600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:223013600-223030800	Weak transcription	Ovary	ovary
5	chr1:223017600-223042400	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:223018200-223029600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:223018200-223029800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:223018200-223031000	Weak transcription	Fetal Kidney	kidney
9	chr1:223018400-223021000	Weak transcription	Brain Anterior Caudate	brain
10	chr1:223018400-223030400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:223019200-223020400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:223019200-223022400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:223019800-223021200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:223019800-223021200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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