Variant report

Variant	rs1408582
Chromosome Location	chr10:91606480-91606481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1125326	0.97[ASN][1000 genomes]
rs11593486	0.81[ASN][1000 genomes]
rs11814174	0.82[CHB][hapmap]
rs12240414	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12244597	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12252414	0.97[ASN][1000 genomes]
rs12265484	0.91[CEU][hapmap]
rs12763878	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12763984	0.97[ASN][1000 genomes]
rs12766364	0.97[ASN][1000 genomes]
rs12770938	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773439	0.97[ASN][1000 genomes]
rs12775585	0.82[EUR][1000 genomes]
rs1326198	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1326199	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128049	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128178	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17385594	0.90[CEU][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1998643	0.81[ASN][1000 genomes]
rs2148276	0.97[ASN][1000 genomes]
rs2181946	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182397	0.97[ASN][1000 genomes]
rs34395627	0.97[ASN][1000 genomes]
rs34407717	0.97[ASN][1000 genomes]
rs34498741	0.97[ASN][1000 genomes]
rs34498979	0.97[ASN][1000 genomes]
rs34768430	0.81[ASN][1000 genomes]
rs34833458	0.97[ASN][1000 genomes]
rs35305443	0.97[ASN][1000 genomes]
rs35495765	0.97[ASN][1000 genomes]
rs35557724	0.97[ASN][1000 genomes]
rs35569149	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35606974	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35762262	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35768372	0.95[ASN][1000 genomes]
rs36067049	0.97[ASN][1000 genomes]
rs36075457	0.97[ASN][1000 genomes]
rs3740040	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3802651	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55932503	0.93[ASN][1000 genomes]
rs55977662	0.97[ASN][1000 genomes]
rs56246606	0.97[ASN][1000 genomes]
rs56318801	0.97[ASN][1000 genomes]
rs57160906	0.97[ASN][1000 genomes]
rs57585079	0.97[ASN][1000 genomes]
rs57603165	0.97[ASN][1000 genomes]
rs58250931	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58929000	0.97[ASN][1000 genomes]
rs58933281	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60925336	0.97[ASN][1000 genomes]
rs61128077	0.97[ASN][1000 genomes]
rs61303211	0.97[ASN][1000 genomes]
rs61646033	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61869791	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61869800	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61869806	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583662	0.91[CEU][hapmap]
rs68147789	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7076194	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7083051	0.91[CEU][hapmap]
rs7098084	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7475158	0.97[ASN][1000 genomes]
rs7895851	0.91[CEU][hapmap]
rs7895863	0.83[CEU][hapmap]
rs7899499	0.91[CEU][hapmap]
rs7908779	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908953	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7912390	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918018	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046241	chr10:91478562-91614437	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv869080	chr10:91498641-91712834	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1036581	chr10:91526705-91691536	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1043571	chr10:91568555-92036154	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv551874	chr10:91570211-92036154	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv949678	chr10:91589048-92016474	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs1408582	KIF20B	cis	cerebellum	SCAN
rs1408582	RP11-248C1.3	cis	Artery Tibial	GTEx
rs1408582	LINC00865	cis	Skin Sun Exposed Lower leg	GTEx
rs1408582	RP11-248C1.3	cis	Esophagus Muscularis	GTEx
rs1408582	LINC00865	cis	Artery Tibial	GTEx
rs1408582	LINC00865	cis	Adipose Subcutaneous	GTEx
rs1408582	RP11-248C1.3	cis	lung	GTEx
rs1408582	RP11-248C1.3	cis	Thyroid	GTEx
rs1408582	LINC00865	cis	Artery Aorta	GTEx
rs1408582	LINC00865	cis	Thyroid	GTEx
rs1408582	LINC00865	cis	lung	GTEx
rs1408582	RP11-248C1.3	cis	Artery Aorta	GTEx
rs1408582	LINC00865	cis	Nerve Tibial	GTEx
rs1408582	HTR7	cis	parietal	SCAN
rs1408582	RP11-248C1.3	cis	Adipose Subcutaneous	GTEx
rs1408582	KIF20B	cis	parietal	SCAN
rs1408582	RP11-248C1.3	cis	Nerve Tibial	GTEx
rs1408582	SNCG	cis	parietal	SCAN
rs1408582	LINC00865	cis	Esophagus Muscularis	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91605400-91606600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr10:91605400-91607000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:91605400-91607000	Enhancers	HMEC	breast
4	chr10:91605600-91606600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:91605600-91606600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:91605600-91606600	Enhancers	Hela-S3	cervix
7	chr10:91605600-91606800	Enhancers	NHEK	skin
8	chr10:91605600-91607000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr10:91605600-91607000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr10:91605600-91607000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr10:91605800-91606600	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr10:91606000-91606600	Enhancers	NH-A	brain
13	chr10:91606000-91606800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr10:91606000-91606800	Enhancers	HepG2	liver
15	chr10:91606000-91607000	Enhancers	H9 Cell Line	embryonic stem cell
16	chr10:91606000-91607000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr10:91606200-91606600	Enhancers	Fetal Intestine Large	intestine
18	chr10:91606200-91607200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr10:91606400-91606600	Enhancers	Fetal Intestine Small	intestine
20	chr10:91606400-91607000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr10:91606400-91607000	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links