Variant report

Variant	rs981230
Chromosome Location	chr5:59039858-59039859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10043265	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs10043283	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10514857	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949859	0.89[ASN][1000 genomes]
rs12152908	0.83[ASN][1000 genomes]
rs12187752	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs12188131	0.93[ASN][1000 genomes]
rs13155799	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1362941	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs1362942	0.93[ASN][1000 genomes]
rs1370230	0.80[TSI][hapmap]
rs1437124	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1504982	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1504984	0.86[ASN][1000 genomes]
rs16877195	0.83[CHB][hapmap];0.86[CHD][hapmap];0.93[ASN][1000 genomes]
rs17369708	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs17381667	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs17381695	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs17381723	0.86[ASN][1000 genomes]
rs17382202	0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[ASN][1000 genomes]
rs17440909	0.83[CHB][hapmap]
rs17441217	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs17441825	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs17742120	0.83[CHB][hapmap];0.82[CHD][hapmap];0.90[ASN][1000 genomes]
rs17742544	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[ASN][1000 genomes]
rs17743216	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs17799161	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs1992112	0.85[TSI][hapmap]
rs2164660	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs28583502	0.89[ASN][1000 genomes]
rs2938780	0.87[MEX][hapmap]
rs2963826	0.87[MEX][hapmap]
rs298067	0.80[TSI][hapmap]
rs3898713	0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs4577665	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4699942	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs4699943	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs4700340	0.83[CHB][hapmap];0.81[CHD][hapmap];0.93[ASN][1000 genomes]
rs4700341	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55704150	0.89[ASN][1000 genomes]
rs55868825	0.93[ASN][1000 genomes]
rs56199003	0.93[ASN][1000 genomes]
rs6450528	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450530	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6860907	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6874708	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[ASN][1000 genomes]
rs6897073	0.83[CHB][hapmap];0.86[CHD][hapmap];0.93[ASN][1000 genomes]
rs72751211	0.89[ASN][1000 genomes]
rs72751218	0.89[ASN][1000 genomes]
rs72751226	0.90[ASN][1000 genomes]
rs72751229	0.93[ASN][1000 genomes]
rs72751231	0.93[ASN][1000 genomes]
rs72751232	0.93[ASN][1000 genomes]
rs72751233	0.93[ASN][1000 genomes]
rs72751234	0.93[ASN][1000 genomes]
rs72751235	0.93[ASN][1000 genomes]
rs72751237	0.93[ASN][1000 genomes]
rs72751241	0.93[ASN][1000 genomes]
rs72751244	0.93[ASN][1000 genomes]
rs72751247	0.93[ASN][1000 genomes]
rs72751250	0.93[ASN][1000 genomes]
rs72751252	0.90[ASN][1000 genomes]
rs72751264	0.84[ASN][1000 genomes]
rs756211	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs756212	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs7701573	0.85[TSI][hapmap]
rs7701748	0.85[TSI][hapmap]
rs7708952	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7710199	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736817	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs877745	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1034283	chr5:58940594-59040762	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv537767	chr5:58940594-59040762	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59021200-59040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:59028000-59043200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:59032800-59040800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:59036800-59040400	Enhancers	A549	lung
5	chr5:59036800-59041600	Enhancers	Hela-S3	cervix
6	chr5:59038800-59041000	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr5:59039400-59041200	Enhancers	Brain Germinal Matrix	brain
8	chr5:59039400-59042600	Enhancers	HMEC	breast
9	chr5:59039400-59059800	Weak transcription	Primary B cells from cord blood	blood
10	chr5:59039600-59040200	Enhancers	NHEK	skin
11	chr5:59039600-59043000	Enhancers	HUVEC	blood vessel
12	chr5:59039800-59040000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:59039800-59040000	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr5:59039800-59040400	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:59039800-59040600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:59039800-59040800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:59039800-59042600	Enhancers	Rectal Smooth Muscle	rectum
18	chr5:59039800-59042600	Enhancers	NH-A	brain

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