Variant report

Variant	rs2408659
Chromosome Location	chr13:53283900-53283901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 240 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:229)

rs_ID	r²[population]
rs1036452	1.00[EUR][1000 genomes]
rs11148261	1.00[EUR][1000 genomes]
rs11148262	1.00[EUR][1000 genomes]
rs1370082	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1370083	1.00[EUR][1000 genomes]
rs1436724	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1436725	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1436728	1.00[EUR][1000 genomes]
rs1436729	1.00[EUR][1000 genomes]
rs186900	1.00[EUR][1000 genomes]
rs1925135	1.00[EUR][1000 genomes]
rs1978805	1.00[EUR][1000 genomes]
rs2033680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2033684	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2033685	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2099547	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2118093	0.94[EUR][1000 genomes]
rs237106	1.00[EUR][1000 genomes]
rs2575957	0.87[EUR][1000 genomes]
rs2575958	1.00[EUR][1000 genomes]
rs2575975	0.97[EUR][1000 genomes]
rs2760755	0.88[EUR][1000 genomes]
rs2760780	1.00[EUR][1000 genomes]
rs342769	1.00[EUR][1000 genomes]
rs342772	1.00[EUR][1000 genomes]
rs342773	1.00[EUR][1000 genomes]
rs342774	1.00[EUR][1000 genomes]
rs342777	1.00[EUR][1000 genomes]
rs34385713	0.83[EUR][1000 genomes]
rs3931491	1.00[EUR][1000 genomes]
rs3989920	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4261418	1.00[EUR][1000 genomes]
rs4261419	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4278636	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4539485	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4542538	1.00[EUR][1000 genomes]
rs4586310	1.00[EUR][1000 genomes]
rs4884223	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4884240	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4885767	1.00[EUR][1000 genomes]
rs4885804	1.00[EUR][1000 genomes]
rs4885827	1.00[EUR][1000 genomes]
rs4885887	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885910	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58007072	1.00[EUR][1000 genomes]
rs58093707	1.00[EUR][1000 genomes]
rs58762582	0.93[EUR][1000 genomes]
rs596546	1.00[EUR][1000 genomes]
rs60117820	1.00[EUR][1000 genomes]
rs601596	1.00[EUR][1000 genomes]
rs602743	1.00[EUR][1000 genomes]
rs60277273	1.00[EUR][1000 genomes]
rs602954	1.00[EUR][1000 genomes]
rs603070	1.00[EUR][1000 genomes]
rs60623593	1.00[EUR][1000 genomes]
rs61311520	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs615509	1.00[EUR][1000 genomes]
rs617660	1.00[EUR][1000 genomes]
rs61958087	1.00[EUR][1000 genomes]
rs61958115	1.00[EUR][1000 genomes]
rs61958120	0.93[EUR][1000 genomes]
rs61958121	1.00[EUR][1000 genomes]
rs61958122	0.94[EUR][1000 genomes]
rs61958123	1.00[EUR][1000 genomes]
rs61958126	1.00[EUR][1000 genomes]
rs61958127	0.90[EUR][1000 genomes]
rs61958131	1.00[EUR][1000 genomes]
rs61958132	1.00[EUR][1000 genomes]
rs61958134	1.00[EUR][1000 genomes]
rs61958135	1.00[EUR][1000 genomes]
rs61958136	1.00[EUR][1000 genomes]
rs61958137	1.00[EUR][1000 genomes]
rs61958139	0.93[EUR][1000 genomes]
rs61958141	1.00[EUR][1000 genomes]
rs61958142	1.00[EUR][1000 genomes]
rs61959576	0.90[EUR][1000 genomes]
rs61959578	1.00[EUR][1000 genomes]
rs61959579	0.93[EUR][1000 genomes]
rs61959591	0.93[EUR][1000 genomes]
rs61959592	0.93[EUR][1000 genomes]
rs61959594	0.93[EUR][1000 genomes]
rs61959595	0.93[EUR][1000 genomes]
rs61959616	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61959617	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61959618	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61959619	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61959620	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61959653	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61959654	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61959656	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61959659	0.87[EUR][1000 genomes]
rs61961160	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs630180	1.00[EUR][1000 genomes]
rs630232	1.00[EUR][1000 genomes]
rs630892	1.00[EUR][1000 genomes]
rs632146	1.00[EUR][1000 genomes]
rs632528	1.00[EUR][1000 genomes]
rs636035	1.00[EUR][1000 genomes]
rs636509	0.97[EUR][1000 genomes]
rs636511	0.97[EUR][1000 genomes]
rs646144	1.00[EUR][1000 genomes]
rs646498	1.00[EUR][1000 genomes]
rs646911	1.00[EUR][1000 genomes]
rs647377	1.00[EUR][1000 genomes]
rs6561672	1.00[EUR][1000 genomes]
rs6561673	0.94[EUR][1000 genomes]
rs6561674	1.00[EUR][1000 genomes]
rs6561676	1.00[EUR][1000 genomes]
rs6561677	1.00[EUR][1000 genomes]
rs6561678	0.97[EUR][1000 genomes]
rs6561679	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6561684	1.00[EUR][1000 genomes]
rs6561685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6561686	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs659247	1.00[EUR][1000 genomes]
rs659848	0.93[EUR][1000 genomes]
rs662582	0.83[EUR][1000 genomes]
rs664827	0.93[EUR][1000 genomes]
rs670291	1.00[EUR][1000 genomes]
rs676306	1.00[EUR][1000 genomes]
rs681165	1.00[EUR][1000 genomes]
rs682343	1.00[EUR][1000 genomes]
rs693991	1.00[EUR][1000 genomes]
rs694275	1.00[EUR][1000 genomes]
rs694846	1.00[EUR][1000 genomes]
rs695165	1.00[EUR][1000 genomes]
rs7319451	1.00[EUR][1000 genomes]
rs7325840	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7330193	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7330361	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7330755	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7335270	1.00[EUR][1000 genomes]
rs7982285	1.00[EUR][1000 genomes]
rs7986540	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7986877	1.00[EUR][1000 genomes]
rs7987162	1.00[EUR][1000 genomes]
rs7987405	0.97[EUR][1000 genomes]
rs7988145	1.00[EUR][1000 genomes]
rs7991651	0.86[EUR][1000 genomes]
rs7992165	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7994651	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7995188	1.00[EUR][1000 genomes]
rs7996692	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7999466	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8000715	1.00[EUR][1000 genomes]
rs893070	1.00[EUR][1000 genomes]
rs9316581	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316582	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316583	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9526947	0.93[EUR][1000 genomes]
rs9526948	0.93[EUR][1000 genomes]
rs9526949	1.00[EUR][1000 genomes]
rs9526957	0.93[EUR][1000 genomes]
rs9526958	1.00[EUR][1000 genomes]
rs9526960	0.93[EUR][1000 genomes]
rs9526964	0.93[EUR][1000 genomes]
rs9526966	0.93[EUR][1000 genomes]
rs9526970	1.00[EUR][1000 genomes]
rs9526972	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9526973	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9526976	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9526978	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9526986	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9526987	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9526988	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9526991	0.87[EUR][1000 genomes]
rs9526993	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9526994	0.87[EUR][1000 genomes]
rs9526997	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536153	0.80[EUR][1000 genomes]
rs9536167	1.00[EUR][1000 genomes]
rs9536168	1.00[EUR][1000 genomes]
rs9536169	0.86[EUR][1000 genomes]
rs9536170	0.90[EUR][1000 genomes]
rs9536171	0.81[EUR][1000 genomes]
rs9536175	0.90[EUR][1000 genomes]
rs9536176	1.00[EUR][1000 genomes]
rs9536177	1.00[EUR][1000 genomes]
rs9536179	1.00[EUR][1000 genomes]
rs9536180	1.00[EUR][1000 genomes]
rs9536181	1.00[EUR][1000 genomes]
rs9536182	1.00[EUR][1000 genomes]
rs9536183	1.00[EUR][1000 genomes]
rs9536184	1.00[EUR][1000 genomes]
rs9536187	1.00[EUR][1000 genomes]
rs9536188	0.97[EUR][1000 genomes]
rs9536189	0.91[EUR][1000 genomes]
rs9536192	1.00[EUR][1000 genomes]
rs9536193	1.00[EUR][1000 genomes]
rs9536194	1.00[EUR][1000 genomes]
rs9536195	1.00[EUR][1000 genomes]
rs9536196	0.93[EUR][1000 genomes]
rs9536205	0.93[EUR][1000 genomes]
rs9536206	0.93[EUR][1000 genomes]
rs9536209	1.00[EUR][1000 genomes]
rs9536215	0.93[EUR][1000 genomes]
rs9536216	1.00[EUR][1000 genomes]
rs9536218	0.93[EUR][1000 genomes]
rs9536221	0.90[EUR][1000 genomes]
rs9536222	1.00[EUR][1000 genomes]
rs9536228	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9536229	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536232	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536233	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536235	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9536237	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536238	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536240	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9536241	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9536243	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9536244	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9536246	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536248	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536249	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9536251	0.87[EUR][1000 genomes]
rs9536255	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536256	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536257	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536260	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536261	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536264	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9536266	1.00[AMR][1000 genomes]
rs9568748	1.00[EUR][1000 genomes]
rs9568752	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9596671	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs964946	1.00[EUR][1000 genomes]
rs971513	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs973198	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1044949	chr13:53071140-53289426	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1044051	chr13:53139132-53287023	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1038942	chr13:53139132-53289426	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1039911	chr13:53139132-53303074	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1037189	chr13:53173013-53287060	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv541775	chr13:53173013-53287060	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1047265	chr13:53173013-53311419	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv541776	chr13:53173013-53311419	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2408659	CKAP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53256600-53297800	Weak transcription	Pancreas	Pancrea
2	chr13:53260800-53297000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr13:53261000-53285200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr13:53262600-53285600	Weak transcription	HMEC	breast
5	chr13:53263400-53285400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:53272400-53297400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr13:53274200-53285400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr13:53276200-53284600	Weak transcription	Fetal Muscle Leg	muscle
9	chr13:53278000-53284600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr13:53278400-53284400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr13:53278400-53285200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr13:53280400-53285400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr13:53280400-53287400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr13:53280600-53294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr13:53280800-53286000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr13:53280800-53286400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr13:53281200-53286200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:53283400-53294600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr13:53283600-53285400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr13:53283600-53286800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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