Variant report

Variant	rs1035516
Chromosome Location	chr5:42823799-42823800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1046068	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10462041	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10941585	0.80[ASN][1000 genomes]
rs10941586	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10941587	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10941591	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10941592	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10941593	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11952526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11953554	0.87[AMR][1000 genomes]
rs11953691	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11957181	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11958761	0.88[AMR][1000 genomes]
rs12054838	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12055087	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12055266	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12187466	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12187996	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs12516157	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12516954	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12517112	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12518414	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12519443	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12519532	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12520759	0.87[AMR][1000 genomes]
rs12521615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12522458	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13178745	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1364024	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1364026	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1364027	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423649	0.82[AMR][1000 genomes]
rs1423652	0.80[AMR][1000 genomes]
rs1423654	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1593070	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1862628	0.91[CEU][hapmap]
rs2113086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2161600	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28919269	0.88[EUR][1000 genomes]
rs28919892	0.91[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28919916	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2973028	0.81[EUR][1000 genomes]
rs35896631	0.87[AMR][1000 genomes]
rs3797310	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3797311	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3849695	0.80[AMR][1000 genomes]
rs3866438	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3870358	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3870359	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3906418	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4143864	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4242120	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4242121	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4866797	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4866798	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4866799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4866802	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4866804	0.87[AMR][1000 genomes]
rs4866805	0.84[AMR][1000 genomes]
rs4866806	0.87[AMR][1000 genomes]
rs4866949	0.90[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap]
rs4866954	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4866958	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4866959	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4866961	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4866962	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4866963	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4866966	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4866967	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55651065	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55660133	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55687632	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55688895	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55801363	0.80[ASN][1000 genomes]
rs56273800	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56394865	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56848171	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58394380	0.84[AMR][1000 genomes]
rs58429632	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59073137	0.86[AMR][1000 genomes]
rs59184964	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60008560	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61099053	0.86[AMR][1000 genomes]
rs61371942	0.86[AMR][1000 genomes]
rs62370873	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62370874	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62370911	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62370912	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62370950	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62370951	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62370952	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62370953	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62370955	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62370959	0.87[AMR][1000 genomes]
rs62372042	0.82[EUR][1000 genomes]
rs62373001	0.80[ASN][1000 genomes]
rs62373002	0.80[ASN][1000 genomes]
rs6865453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6875431	0.91[YRI][hapmap]
rs6880056	0.82[AMR][1000 genomes]
rs6882786	0.82[AMR][1000 genomes]
rs6886900	0.91[YRI][hapmap]
rs6889614	0.91[YRI][hapmap]
rs6896902	0.80[AMR][1000 genomes]
rs6899268	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs722677	0.81[ASN][1000 genomes]
rs722678	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7579	0.87[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7703376	0.87[AMR][1000 genomes]
rs7708223	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.80[ASN][1000 genomes]
rs7708337	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7719242	0.87[AMR][1000 genomes]
rs7725776	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.80[ASN][1000 genomes]
rs7725961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7730190	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7734918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7735857	0.82[AMR][1000 genomes]
rs8180394	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8180482	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs882775	0.87[AMR][1000 genomes]
rs9637794	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9687651	0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1035516	OXCT1	cis	parietal	SCAN
rs1035516	CCDC152	cis	Artery Tibial	GTEx
rs1035516	CCDC152	cis	Artery Aorta	GTEx
rs1035516	SEPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42813200-42824400	Weak transcription	Adipose Nuclei	Adipose
2	chr5:42817000-42827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:42821400-42826000	Weak transcription	Fetal Stomach	stomach
4	chr5:42822800-42825800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:42823200-42826400	Enhancers	Fetal Intestine Small	intestine
6	chr5:42823400-42826200	Flanking Active TSS	Liver	Liver
7	chr5:42823400-42826400	Flanking Active TSS	HepG2	liver
8	chr5:42823600-42826200	Enhancers	Fetal Intestine Large	intestine

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