Variant report

Variant	rs2939533
Chromosome Location	chr5:145564409-145564410
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:145562850..145566563-chr5:145571128..145574037,3	MCF-7	breast:
2	chr5:145563092..145566274-chr5:145579879..145584548,5	MCF-7	breast:
3	chr5:145560592..145565120-chr5:145580444..145584486,7	K562	blood:

Variant related genes	Relation type
ENSG00000091009	Chromatin interaction

Extended variants
information (count: 287 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:282)

rs_ID	r²[population]
rs1006204	0.82[EUR][1000 genomes]
rs10515564	0.88[ASN][1000 genomes]
rs10515565	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10515566	0.81[ASN][1000 genomes]
rs1054020	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10988	0.84[ASN][1000 genomes]
rs1115080	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11167931	0.84[ASN][1000 genomes]
rs11167932	0.88[ASN][1000 genomes]
rs11167933	0.88[ASN][1000 genomes]
rs11167934	0.88[ASN][1000 genomes]
rs11167936	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11540214	0.88[ASN][1000 genomes]
rs11540215	1.00[ASN][1000 genomes]
rs11540217	0.88[ASN][1000 genomes]
rs11948016	1.00[ASN][1000 genomes]
rs11948180	0.88[ASN][1000 genomes]
rs11948314	0.88[ASN][1000 genomes]
rs11949351	1.00[ASN][1000 genomes]
rs11949703	0.88[ASN][1000 genomes]
rs11950903	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11951553	0.88[ASN][1000 genomes]
rs11952228	0.84[ASN][1000 genomes]
rs11953506	0.82[ASN][1000 genomes]
rs11953517	0.85[ASN][1000 genomes]
rs11954083	0.88[ASN][1000 genomes]
rs11954750	0.88[ASN][1000 genomes]
rs11954870	0.88[ASN][1000 genomes]
rs11954923	0.88[ASN][1000 genomes]
rs11954977	0.88[ASN][1000 genomes]
rs11955443	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11955557	0.99[ASN][1000 genomes]
rs11955635	0.86[ASN][1000 genomes]
rs11957830	1.00[ASN][1000 genomes]
rs11957888	1.00[ASN][1000 genomes]
rs11957998	1.00[ASN][1000 genomes]
rs11958136	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11958216	0.94[ASN][1000 genomes]
rs11959805	0.86[ASN][1000 genomes]
rs12152830	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12153109	0.86[ASN][1000 genomes]
rs12153238	0.88[ASN][1000 genomes]
rs12186358	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12187277	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12188066	0.82[EUR][1000 genomes]
rs12188772	1.00[ASN][1000 genomes]
rs12189385	0.84[ASN][1000 genomes]
rs13153675	0.88[ASN][1000 genomes]
rs13153891	0.85[ASN][1000 genomes]
rs13154547	0.88[ASN][1000 genomes]
rs13154735	1.00[ASN][1000 genomes]
rs13157279	1.00[ASN][1000 genomes]
rs13159380	1.00[ASN][1000 genomes]
rs13160605	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13160905	0.86[ASN][1000 genomes]
rs13161036	1.00[ASN][1000 genomes]
rs13161075	0.88[ASN][1000 genomes]
rs13161488	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13161659	0.86[ASN][1000 genomes]
rs13162175	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13162233	0.82[ASN][1000 genomes]
rs13162640	0.86[ASN][1000 genomes]
rs13164882	0.88[ASN][1000 genomes]
rs13168967	0.84[ASN][1000 genomes]
rs13169370	0.85[ASN][1000 genomes]
rs13171596	1.00[ASN][1000 genomes]
rs13171828	0.80[ASN][1000 genomes]
rs13171939	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13172010	0.82[ASN][1000 genomes]
rs13173347	0.82[ASN][1000 genomes]
rs13174055	0.82[ASN][1000 genomes]
rs13175587	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13176784	1.00[ASN][1000 genomes]
rs13176915	1.00[ASN][1000 genomes]
rs13177015	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13178370	0.88[ASN][1000 genomes]
rs13178443	0.83[ASN][1000 genomes]
rs13178516	0.88[ASN][1000 genomes]
rs13178755	1.00[ASN][1000 genomes]
rs13178840	0.86[ASN][1000 genomes]
rs13179296	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13179517	1.00[ASN][1000 genomes]
rs13180113	0.88[ASN][1000 genomes]
rs13182567	0.88[ASN][1000 genomes]
rs13183541	0.85[ASN][1000 genomes]
rs13183976	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13184702	0.88[ASN][1000 genomes]
rs13185518	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13185586	1.00[ASN][1000 genomes]
rs13185805	0.87[ASN][1000 genomes]
rs13186694	0.88[ASN][1000 genomes]
rs13186701	1.00[ASN][1000 genomes]
rs1368345	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1395276	0.86[ASN][1000 genomes]
rs1395277	0.86[ASN][1000 genomes]
rs1506431	0.98[ASN][1000 genomes]
rs1567057	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17096590	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17104255	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17426845	0.84[ASN][1000 genomes]
rs17427286	0.86[ASN][1000 genomes]
rs17427691	0.88[ASN][1000 genomes]
rs17428100	0.88[ASN][1000 genomes]
rs17428465	0.88[ASN][1000 genomes]
rs17428570	0.88[ASN][1000 genomes]
rs17428647	1.00[ASN][1000 genomes]
rs17428724	1.00[ASN][1000 genomes]
rs17429180	0.84[ASN][1000 genomes]
rs17492851	0.86[ASN][1000 genomes]
rs17492893	0.86[ASN][1000 genomes]
rs17492950	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17493090	0.86[ASN][1000 genomes]
rs17493851	0.88[ASN][1000 genomes]
rs17500456	0.88[ASN][1000 genomes]
rs17500483	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17500504	0.88[ASN][1000 genomes]
rs17500927	1.00[ASN][1000 genomes]
rs17501177	0.84[ASN][1000 genomes]
rs17501601	0.81[ASN][1000 genomes]
rs1864948	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1876189	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1911112	0.88[ASN][1000 genomes]
rs1911113	0.88[ASN][1000 genomes]
rs2014462	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2014473	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2015248	0.82[ASN][1000 genomes]
rs2024056	0.82[EUR][1000 genomes]
rs2063002	1.00[ASN][1000 genomes]
rs2063005	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2279895	0.96[ASN][1000 genomes]
rs2292172	0.88[ASN][1000 genomes]
rs2292173	0.88[ASN][1000 genomes]
rs2400209	0.84[ASN][1000 genomes]
rs2895647	0.86[ASN][1000 genomes]
rs2895648	0.86[ASN][1000 genomes]
rs2895649	0.86[ASN][1000 genomes]
rs2895650	0.88[ASN][1000 genomes]
rs2939535	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2939536	0.88[ASN][1000 genomes]
rs2939539	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2962502	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2962503	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2962509	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2962510	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2962511	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2962515	1.00[ASN][1000 genomes]
rs2963914	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2963915	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2963918	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2963919	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2963920	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2963921	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2963922	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2963923	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2963924	0.88[ASN][1000 genomes]
rs2963926	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33914983	1.00[ASN][1000 genomes]
rs34014355	1.00[ASN][1000 genomes]
rs34049009	0.88[ASN][1000 genomes]
rs34082425	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34141601	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34272709	0.88[ASN][1000 genomes]
rs34342344	0.88[ASN][1000 genomes]
rs34345997	0.88[ASN][1000 genomes]
rs34404385	0.88[ASN][1000 genomes]
rs34405762	1.00[ASN][1000 genomes]
rs34444119	0.84[ASN][1000 genomes]
rs34461274	0.86[ASN][1000 genomes]
rs34482773	0.88[ASN][1000 genomes]
rs34519824	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34529192	0.88[ASN][1000 genomes]
rs34533649	0.98[ASN][1000 genomes]
rs34581962	0.88[ASN][1000 genomes]
rs34672485	0.88[ASN][1000 genomes]
rs34683303	0.86[ASN][1000 genomes]
rs34774165	0.86[ASN][1000 genomes]
rs34794113	0.88[ASN][1000 genomes]
rs34794547	0.88[ASN][1000 genomes]
rs34812645	0.83[ASN][1000 genomes]
rs35048100	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35048686	1.00[ASN][1000 genomes]
rs35170264	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35238125	0.88[ASN][1000 genomes]
rs35262581	0.88[ASN][1000 genomes]
rs35369194	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35421100	1.00[ASN][1000 genomes]
rs35421875	0.85[ASN][1000 genomes]
rs35424128	0.84[ASN][1000 genomes]
rs35436549	0.88[ASN][1000 genomes]
rs35658996	0.88[ASN][1000 genomes]
rs35676277	0.84[ASN][1000 genomes]
rs35749752	0.88[ASN][1000 genomes]
rs35821418	0.88[ASN][1000 genomes]
rs35825928	0.86[ASN][1000 genomes]
rs35868039	0.88[ASN][1000 genomes]
rs35869904	0.88[ASN][1000 genomes]
rs35935643	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35947468	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36019024	0.86[ASN][1000 genomes]
rs36059140	0.88[ASN][1000 genomes]
rs36095232	0.88[ASN][1000 genomes]
rs36098188	0.88[ASN][1000 genomes]
rs36102990	0.88[ASN][1000 genomes]
rs36122632	0.88[ASN][1000 genomes]
rs3749994	0.86[ASN][1000 genomes]
rs3763373	0.88[ASN][1000 genomes]
rs3797628	0.88[ASN][1000 genomes]
rs3822623	0.88[ASN][1000 genomes]
rs3828935	0.88[ASN][1000 genomes]
rs3937558	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4413574	1.00[ASN][1000 genomes]
rs4443471	1.00[ASN][1000 genomes]
rs4705119	0.88[ASN][1000 genomes]
rs4705156	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4705398	0.88[ASN][1000 genomes]
rs4705438	0.88[ASN][1000 genomes]
rs4705445	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4913064	0.81[ASN][1000 genomes]
rs4913065	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4913066	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4913067	0.82[ASN][1000 genomes]
rs55665974	1.00[ASN][1000 genomes]
rs55681213	0.88[ASN][1000 genomes]
rs55799797	0.98[ASN][1000 genomes]
rs55812375	0.86[ASN][1000 genomes]
rs55909935	1.00[ASN][1000 genomes]
rs55937908	0.82[ASN][1000 genomes]
rs56240028	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56278005	0.84[ASN][1000 genomes]
rs56338615	1.00[ASN][1000 genomes]
rs56410805	1.00[ASN][1000 genomes]
rs56413906	0.84[EUR][1000 genomes]
rs58848845	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62372773	0.83[EUR][1000 genomes]
rs62373771	0.83[ASN][1000 genomes]
rs62373785	0.88[ASN][1000 genomes]
rs62373786	0.88[ASN][1000 genomes]
rs62373789	0.88[ASN][1000 genomes]
rs62373798	0.88[ASN][1000 genomes]
rs62373799	0.86[ASN][1000 genomes]
rs62373801	0.88[ASN][1000 genomes]
rs62373802	0.88[ASN][1000 genomes]
rs62373809	1.00[ASN][1000 genomes]
rs62373810	1.00[ASN][1000 genomes]
rs62373811	1.00[ASN][1000 genomes]
rs62373812	1.00[ASN][1000 genomes]
rs62373813	0.99[ASN][1000 genomes]
rs62373819	1.00[ASN][1000 genomes]
rs62373823	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62373824	0.98[ASN][1000 genomes]
rs62373831	0.85[ASN][1000 genomes]
rs6580408	0.83[EUR][1000 genomes]
rs6580413	0.85[EUR][1000 genomes]
rs66538287	0.88[ASN][1000 genomes]
rs67051761	0.88[ASN][1000 genomes]
rs67598659	0.88[ASN][1000 genomes]
rs67986716	0.87[ASN][1000 genomes]
rs6861532	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6862371	0.82[EUR][1000 genomes]
rs6867146	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6868728	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6870878	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6878005	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6881180	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6882517	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6884493	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6892928	0.82[EUR][1000 genomes]
rs6893994	0.81[EUR][1000 genomes]
rs71594528	1.00[ASN][1000 genomes]
rs72822286	0.88[ASN][1000 genomes]
rs7443214	1.00[ASN][1000 genomes]
rs7702123	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7703269	0.87[EUR][1000 genomes]
rs7711896	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7722258	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7724811	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7727353	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7728381	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7728631	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7729098	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9918101	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9918130	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv883006	chr5:145450586-145672431	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428128	chr5:145503978-145682880	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv883007	chr5:145506100-145672431	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv883008	chr5:145509728-145642925	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3348501	chr5:145543808-145572250	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2939533	LARS	cis	Thyroid	GTEx
rs2939533	LARS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145562800-145569800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:145563000-145564600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:145563000-145564600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:145563000-145564600	Weak transcription	A549	lung
5	chr5:145563000-145564600	Weak transcription	HMEC	breast
6	chr5:145563000-145564600	Weak transcription	HUVEC	blood vessel
7	chr5:145563000-145564600	Weak transcription	NHDF-Ad	bronchial
8	chr5:145563000-145564600	Weak transcription	NHEK	skin
9	chr5:145563000-145564600	Weak transcription	Osteobl	bone
10	chr5:145563000-145564800	Weak transcription	NH-A	brain
11	chr5:145563000-145565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:145563000-145568000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:145563000-145568800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:145563000-145582200	Weak transcription	Right Atrium	heart
15	chr5:145563200-145564600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:145563200-145564600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:145563200-145564600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:145563200-145564800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:145563400-145566800	Weak transcription	Placenta	Placenta
20	chr5:145563400-145570600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links