Variant report

Variant	rs11725409
Chromosome Location	chr4:120288850-120288851
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11722431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722940	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11724619	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11728178	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11729960	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11733667	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11734624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734808	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11736997	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11737068	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13101369	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13112320	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13122306	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13127517	0.83[EUR][1000 genomes]
rs13128673	0.84[ASN][1000 genomes]
rs13139711	0.92[EUR][1000 genomes]
rs13144426	0.81[EUR][1000 genomes]
rs1397611	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17050312	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17517075	0.83[EUR][1000 genomes]
rs17517470	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17595468	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17595769	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17595790	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2036859	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34125807	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34733524	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34878806	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34951506	0.81[EUR][1000 genomes]
rs35225855	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35612705	0.81[EUR][1000 genomes]
rs35646004	0.81[EUR][1000 genomes]
rs35846514	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35917388	0.82[ASN][1000 genomes]
rs3817230	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3817242	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56818816	0.84[EUR][1000 genomes]
rs58536775	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320715	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320716	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320717	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320718	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320720	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320721	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320722	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320723	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320724	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320725	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320731	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320732	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320733	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320735	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320737	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62320741	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62322274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62322275	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62322276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328404	0.81[EUR][1000 genomes]
rs62328408	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62328420	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6822097	1.00[AFR][1000 genomes]
rs71627784	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72918504	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv964091	chr4:120255342-120290951	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11725409	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs11725409	RP11-33B1.1	cis	Thyroid	GTEx
rs11725409	USP53	cis	Whole Blood	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120269600-120293000	Weak transcription	Fetal Heart	heart
2	chr4:120282600-120290000	Weak transcription	HepG2	liver
3	chr4:120285400-120290000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:120285400-120291600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr4:120285800-120291000	Weak transcription	Primary T cells from cord blood	blood
6	chr4:120286000-120291200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:120288400-120291400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:120288400-120291400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:120288400-120291600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:120288600-120291200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links