Variant report

Variant	rs1781938
Chromosome Location	chr10:5201444-5201445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 141 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10752001	0.85[CHB][hapmap]
rs10752005	0.80[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10795242	0.85[CHB][hapmap]
rs10795245	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10904421	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10904432	1.00[ASN][1000 genomes]
rs11252922	0.85[CHB][hapmap]
rs11253024	1.00[ASN][1000 genomes]
rs11492967	1.00[ASN][1000 genomes]
rs11511661	1.00[ASN][1000 genomes]
rs11511664	1.00[ASN][1000 genomes]
rs11524375	1.00[ASN][1000 genomes]
rs1155931	1.00[ASN][1000 genomes]
rs12355837	1.00[ASN][1000 genomes]
rs12355966	0.97[ASN][1000 genomes]
rs12356304	1.00[ASN][1000 genomes]
rs12387	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs12529	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12775468	0.80[ASN][1000 genomes]
rs12775701	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17134471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17134523	0.85[CHB][hapmap]
rs1761601	1.00[ASN][1000 genomes]
rs1761602	1.00[ASN][1000 genomes]
rs1761603	0.98[ASN][1000 genomes]
rs1761604	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1761606	1.00[ASN][1000 genomes]
rs1781927	0.94[ASN][1000 genomes]
rs1781929	0.98[ASN][1000 genomes]
rs1781930	0.98[ASN][1000 genomes]
rs1781932	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1781933	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781935	1.00[ASN][1000 genomes]
rs1781937	1.00[ASN][1000 genomes]
rs1781939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781940	1.00[ASN][1000 genomes]
rs1781941	0.94[ASN][1000 genomes]
rs1892404	0.80[ASN][1000 genomes]
rs1937840	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1937841	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1937845	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs1937847	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs1937848	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs1937849	1.00[CHB][hapmap]
rs1937882	0.85[ASN][1000 genomes]
rs1937916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2151899	0.91[ASN][1000 genomes]
rs2151900	0.97[ASN][1000 genomes]
rs2154308	0.85[ASN][1000 genomes]
rs2186175	0.85[ASN][1000 genomes]
rs2211630	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2226260	0.80[ASN][1000 genomes]
rs2298305	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs2398103	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2398195	0.80[ASN][1000 genomes]
rs2398196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2518047	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2518049	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2801882	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2801883	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs34573009	0.95[ASN][1000 genomes]
rs34606065	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3750573	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812617	0.85[CHB][hapmap]
rs4242785	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs4330990	0.98[ASN][1000 genomes]
rs4494227	0.91[ASN][1000 genomes]
rs4622159	0.80[ASN][1000 genomes]
rs4880708	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4880710	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4881395	0.83[CHB][hapmap]
rs4881396	0.85[CHB][hapmap]
rs4881397	0.85[CHB][hapmap]
rs4881403	0.83[ASN][1000 genomes]
rs4881404	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4881408	1.00[ASN][1000 genomes]
rs4881410	1.00[ASN][1000 genomes]
rs56312472	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57097292	0.85[AFR][1000 genomes]
rs60878270	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854684	0.98[ASN][1000 genomes]
rs61854686	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61854687	0.98[ASN][1000 genomes]
rs61854697	0.98[ASN][1000 genomes]
rs61854701	0.95[ASN][1000 genomes]
rs61854702	0.95[ASN][1000 genomes]
rs61854705	0.95[ASN][1000 genomes]
rs6601898	0.85[CHB][hapmap]
rs6601899	0.85[CHB][hapmap]
rs6601919	1.00[ASN][1000 genomes]
rs6601920	1.00[ASN][1000 genomes]
rs6601921	1.00[ASN][1000 genomes]
rs6601923	1.00[ASN][1000 genomes]
rs7067921	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7070300	1.00[ASN][1000 genomes]
rs7071406	1.00[ASN][1000 genomes]
rs7072048	0.97[ASN][1000 genomes]
rs7072750	1.00[ASN][1000 genomes]
rs7074004	0.85[CHB][hapmap]
rs7074118	0.85[ASN][1000 genomes]
rs7080497	1.00[ASN][1000 genomes]
rs7084630	0.89[ASN][1000 genomes]
rs7086984	0.80[ASN][1000 genomes]
rs7087111	0.85[CHB][hapmap]
rs7089964	1.00[ASN][1000 genomes]
rs7090038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72478267	0.92[ASN][1000 genomes]
rs7898263	0.85[CHB][hapmap]
rs7898341	1.00[ASN][1000 genomes]
rs7901781	0.85[CHB][hapmap]
rs7902978	1.00[ASN][1000 genomes]
rs7914117	0.80[ASN][1000 genomes]
rs7917079	0.80[ASN][1000 genomes]
rs7918456	1.00[ASN][1000 genomes]
rs7920135	0.80[ASN][1000 genomes]
rs878766	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9731372	0.83[ASN][1000 genomes]
rs9794201	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv549882	chr10:4943518-5203864	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1036566	chr10:5037926-5261426	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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	13 gene(s)	inside rSNPs	diseases
13	nsv549883	chr10:5037926-5275762	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv1047484	chr10:5076258-5261482	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv1036291	chr10:5076258-5456234	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv540465	chr10:5108345-5261482	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv540467	chr10:5114577-5225365	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv540468	chr10:5114577-5261482	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv540469	chr10:5120774-5225365	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv540470	chr10:5120774-5261482	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv540471	chr10:5133561-5261482	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv540472	chr10:5133561-5284334	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
23	nsv1048081	chr10:5149144-5321395	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1781938	TUBAL3	cis	cerebellum	SCAN
rs1781938	H2AFZ	trans	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5194400-5206600	Strong transcription	Liver	Liver
2	chr10:5198000-5202800	Weak transcription	Adipose Nuclei	Adipose
3	chr10:5198200-5207200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:5201400-5201800	Enhancers	HMEC	breast

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