Variant report

Variant	rs11729960
Chromosome Location	chr4:120232458-120232459
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120230931..120233394-chr4:120986011..120987625,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11722431	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11722940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724619	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725409	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11725433	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11727970	0.88[ASN][1000 genomes]
rs11727975	0.88[ASN][1000 genomes]
rs11728178	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733606	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11734624	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11734808	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737068	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737560	0.89[CEU][hapmap]
rs13104050	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13106878	0.90[CEU][hapmap]
rs13112320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113462	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13113662	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13116789	0.90[CEU][hapmap]
rs13122306	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124532	0.90[CEU][hapmap]
rs13127517	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13139711	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13140255	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13144426	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1397611	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511021	0.89[CEU][hapmap]
rs1511022	0.86[CEU][hapmap]
rs17050312	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17334151	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17517075	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17517470	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595769	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595790	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036859	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34125807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34156358	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34733524	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878806	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34951506	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35137697	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35225855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612705	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35646004	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35846514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35917388	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817230	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817242	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56818816	0.95[ASN][1000 genomes]
rs62320715	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320716	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320717	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320718	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320719	0.91[ASN][1000 genomes]
rs62320720	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320721	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320722	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320723	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320724	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320725	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320731	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320732	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320733	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320735	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320737	1.00[ASN][1000 genomes]
rs62322274	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62322275	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62322276	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62328380	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328402	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328403	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328404	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328420	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822097	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71627784	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72918504	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv879840	chr4:120227419-120257417	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11729960	RP11-33B1.1	cis	Thyroid	GTEx
rs11729960	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs11729960	USP53	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120222000-120251000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:120222200-120244600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:120222400-120240800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:120222800-120240800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:120225000-120238800	Weak transcription	Fetal Intestine Small	intestine
6	chr4:120228200-120238600	Weak transcription	Fetal Intestine Large	intestine
7	chr4:120229200-120238400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:120231200-120233000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:120231800-120232800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:120232000-120232600	Enhancers	NH-A	brain
11	chr4:120232000-120232800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:120232000-120232800	Enhancers	Osteobl	bone
13	chr4:120232200-120232800	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links