Variant report

Variant	rs1743471
Chromosome Location	chr20:15120323-15120324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1022757	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs11087123	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs11908639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs13045366	0.90[JPT][hapmap]
rs1657957	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1657969	0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs1734913	0.83[AFR][1000 genomes]
rs1743472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1743473	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1743475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1967749	0.84[ASN][1000 genomes]
rs199294	0.90[JPT][hapmap];0.89[YRI][hapmap]
rs199295	0.89[JPT][hapmap]
rs368368	0.90[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs369438	0.82[AFR][1000 genomes]
rs372586	0.90[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs381723	0.90[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs382050	0.90[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs391454	0.81[AFR][1000 genomes]
rs392143	0.81[AFR][1000 genomes]
rs393367	0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs403365	0.82[AFR][1000 genomes]
rs403949	0.90[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs409678	0.90[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs410068	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs412032	0.82[AFR][1000 genomes]
rs412837	0.80[AFR][1000 genomes]
rs420216	0.81[AFR][1000 genomes]
rs420651	0.81[AFR][1000 genomes]
rs421292	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs431713	0.89[JPT][hapmap]
rs432033	0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs4340602	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs439381	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs440313	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs443355	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs443742	0.82[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap]
rs444687	0.90[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs444709	0.90[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs444907	0.83[AFR][1000 genomes]
rs445251	0.90[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs448432	0.82[AFR][1000 genomes]
rs453600	0.87[GIH][hapmap]
rs455205	0.90[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs456646	0.82[AFR][1000 genomes]
rs458376	0.80[AFR][1000 genomes]
rs459322	0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.89[YRI][hapmap]
rs459874	0.90[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap]
rs4610131	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs461300	0.90[JPT][hapmap];0.89[YRI][hapmap]
rs465491	0.90[JPT][hapmap];0.89[YRI][hapmap]
rs467252	0.82[AFR][1000 genomes]
rs467455	0.82[AFR][1000 genomes]
rs6034110	0.90[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs6074842	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs6079676	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079677	0.82[AFR][1000 genomes]
rs6079678	0.90[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs6110526	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6110528	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6110529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6110532	0.90[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs6110533	0.90[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs6131641	0.82[YRI][hapmap]
rs799179	0.80[GIH][hapmap]
rs808924	0.90[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap]
rs970005	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:71 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066070	chr20:14627662-15180181	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv949548	chr20:14667415-15125972	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv948395	chr20:14667415-15161670	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv916020	chr20:14700045-15134231	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1064871	chr20:14756392-15134217	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv544198	chr20:14756392-15134217	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv585488	chr20:14764611-15150730	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1065152	chr20:14781684-15305258	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv912754	chr20:14817453-15170958	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1057120	chr20:14837251-15166775	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv931936	chr20:14838217-15154763	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv912767	chr20:14854935-15189598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv585540	chr20:14858910-15242365	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv912769	chr20:14872313-15126507	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1066220	chr20:14883338-15204628	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv912774	chr20:14901776-15177309	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1055346	chr20:14910001-15136103	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1057548	chr20:14910001-15172302	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv1060571	chr20:14924247-15139048	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	nsv868936	chr20:14928568-15183054	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv1056236	chr20:14932884-15122642	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv1058717	chr20:14932884-15137154	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv912777	chr20:14936935-15141959	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv1063917	chr20:14939608-15206129	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
25	nsv1058179	chr20:14941259-15136103	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	nsv544205	chr20:14941259-15136103	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
27	nsv912778	chr20:14949763-15207464	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
28	nsv1062252	chr20:14964258-15547739	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
29	nsv544206	chr20:14964258-15547739	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
30	nsv932106	chr20:14964459-15203333	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
31	nsv912780	chr20:14967506-15139048	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
32	nsv1058314	chr20:14978835-15149030	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
33	nsv1060511	chr20:14982565-15157970	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
34	nsv585561	chr20:14992542-15122743	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
35	nsv1062600	chr20:14999727-15128322	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
36	nsv524481	chr20:15007730-15382919	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
37	nsv1067184	chr20:15019429-15136103	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
38	nsv916795	chr20:15041479-15345528	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
39	nsv1062960	chr20:15045757-15204628	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
40	nsv1065647	chr20:15049686-15128322	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
41	nsv1055526	chr20:15049686-15138803	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
42	nsv1065611	chr20:15049686-15179481	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
43	nsv1065831	chr20:15052434-15144763	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
44	nsv1064739	chr20:15052434-15154575	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
45	nsv1063637	chr20:15052434-15154706	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
46	esv2763667	chr20:15052446-15170143	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
47	nsv585569	chr20:15052514-15141004	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
48	nsv516721	chr20:15052514-15143806	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
49	nsv585570	chr20:15052514-15143806	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
50	nsv458924	chr20:15054436-15143806	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1743471	SNX5	cis	parietal	SCAN
rs1743471	BFSP1	cis	parietal	SCAN
rs1743471	ESF1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15119200-15120600	Enhancers	Fetal Intestine Large	intestine
2	chr20:15119600-15125200	Weak transcription	Fetal Heart	heart
3	chr20:15119800-15127400	Weak transcription	Fetal Kidney	kidney
4	chr20:15120000-15120600	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr20:15120000-15120600	Enhancers	Gastric	stomach
6	chr20:15120200-15121200	Weak transcription	Stomach Mucosa	stomach
7	chr20:15120200-15121400	Weak transcription	Fetal Intestine Small	intestine

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