Variant report

Variant	rs12522458
Chromosome Location	chr5:42824625-42824626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 127 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1035516	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1046068	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10462041	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10941586	0.82[EUR][1000 genomes]
rs10941587	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10941591	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10941592	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10941593	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11952526	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11953554	0.89[AMR][1000 genomes]
rs11953691	0.81[EUR][1000 genomes]
rs11957181	0.82[EUR][1000 genomes]
rs11958761	0.90[AMR][1000 genomes]
rs12054838	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12055087	0.87[EUR][1000 genomes]
rs12055266	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12187466	0.82[EUR][1000 genomes]
rs12516157	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12516954	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12517112	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12518414	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12519443	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12519532	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12520759	0.89[AMR][1000 genomes]
rs12521615	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13178745	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1364024	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1364026	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1364027	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1423649	0.85[AMR][1000 genomes]
rs1423651	0.80[AMR][1000 genomes]
rs1423652	0.82[AMR][1000 genomes]
rs1423654	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1593070	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2113086	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2161600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28919269	0.88[EUR][1000 genomes]
rs28919892	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28919916	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2973028	0.81[EUR][1000 genomes]
rs35896631	0.89[AMR][1000 genomes]
rs3797310	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3797311	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3849695	0.83[AMR][1000 genomes]
rs3866438	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3870358	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3870359	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3906418	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4143864	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4242120	0.82[EUR][1000 genomes]
rs4242121	0.82[EUR][1000 genomes]
rs4866794	0.81[EUR][1000 genomes]
rs4866797	0.82[EUR][1000 genomes]
rs4866798	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4866799	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4866802	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4866804	0.89[AMR][1000 genomes]
rs4866805	0.87[AMR][1000 genomes]
rs4866806	0.89[AMR][1000 genomes]
rs4866952	0.81[EUR][1000 genomes]
rs4866954	0.82[EUR][1000 genomes]
rs4866958	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4866959	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4866961	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4866962	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4866963	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4866966	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4866967	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55651065	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55660133	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55687632	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55688895	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56273800	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56394865	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56848171	0.82[EUR][1000 genomes]
rs58394380	0.86[AMR][1000 genomes]
rs58429632	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59073137	0.88[AMR][1000 genomes]
rs59184964	0.89[EUR][1000 genomes]
rs60008560	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61099053	0.88[AMR][1000 genomes]
rs61371942	0.88[AMR][1000 genomes]
rs62370873	0.82[EUR][1000 genomes]
rs62370874	0.82[EUR][1000 genomes]
rs62370911	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62370912	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62370950	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62370951	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62370952	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62370953	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62370955	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62370959	0.89[AMR][1000 genomes]
rs62372042	0.82[EUR][1000 genomes]
rs6865453	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6880056	0.85[AMR][1000 genomes]
rs6882786	0.85[AMR][1000 genomes]
rs6896902	0.83[AMR][1000 genomes]
rs6899268	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs722678	0.82[EUR][1000 genomes]
rs7579	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7703376	0.89[AMR][1000 genomes]
rs7708337	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7719242	0.89[AMR][1000 genomes]
rs7725961	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7734918	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7735857	0.85[AMR][1000 genomes]
rs8180394	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8180482	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs882775	0.89[AMR][1000 genomes]
rs9637794	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9687651	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	8 gene(s)	inside rSNPs	diseases
8	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
9	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
10	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
11	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
14	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
15	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
16	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12522458	SEPP1	Cis_1M	lymphoblastoid	RTeQTL
rs12522458	CCDC152	cis	Artery Aorta	GTEx
rs12522458	CCDC152	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42817000-42827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:42821400-42826000	Weak transcription	Fetal Stomach	stomach
3	chr5:42822800-42825800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr5:42823200-42826400	Enhancers	Fetal Intestine Small	intestine
5	chr5:42823400-42826200	Flanking Active TSS	Liver	Liver
6	chr5:42823400-42826400	Flanking Active TSS	HepG2	liver
7	chr5:42823600-42826200	Enhancers	Fetal Intestine Large	intestine
8	chr5:42824200-42824800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr5:42824200-42826200	Enhancers	Gastric	stomach
10	chr5:42824200-42826400	Enhancers	Pancreas	Pancrea
11	chr5:42824400-42824800	Enhancers	Duodenum Mucosa	Duodenum
12	chr5:42824400-42824800	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr5:42824400-42825000	Enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links