Variant report

Variant	rs12770938
Chromosome Location	chr10:91606212-91606213
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 15 )

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	0.89[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]
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]
rs1408582	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];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	0.96[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	0.84[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	0.96[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	0.84[CEU][hapmap]
rs7908779	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908953	0.96[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	0.84[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12770938	RP11-248C1.3	cis	Adipose Subcutaneous	GTEx
rs12770938	RP11-248C1.3	cis	Nerve Tibial	GTEx
rs12770938	RP11-248C1.3	cis	lung	GTEx
rs12770938	LINC00865	cis	Skin Sun Exposed Lower leg	GTEx
rs12770938	LINC00865	cis	Artery Tibial	GTEx
rs12770938	LINC00865	cis	Adipose Subcutaneous	GTEx
rs12770938	LINC00865	cis	Artery Aorta	GTEx
rs12770938	RP11-248C1.3	cis	Artery Aorta	GTEx
rs12770938	LINC00865	cis	Esophagus Muscularis	GTEx
rs12770938	LINC00865	cis	Thyroid	GTEx
rs12770938	RP11-248C1.3	cis	Artery Tibial	GTEx
rs12770938	LINC00865	cis	Nerve Tibial	GTEx
rs12770938	LINC00865	cis	lung	GTEx
rs12770938	RP11-248C1.3	cis	Thyroid	GTEx
rs12770938	RP11-248C1.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91599200-91606400	Weak transcription	Fetal Intestine Small	intestine
2	chr10:91605400-91606400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:91605400-91606400	Enhancers	Osteobl	bone
4	chr10:91605400-91606600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:91605400-91607000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:91605400-91607000	Enhancers	HMEC	breast
7	chr10:91605600-91606400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr10:91605600-91606400	Enhancers	NHLF	lung
9	chr10:91605600-91606600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr10:91605600-91606600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:91605600-91606600	Enhancers	Hela-S3	cervix
12	chr10:91605600-91606800	Enhancers	NHEK	skin
13	chr10:91605600-91607000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr10:91605600-91607000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr10:91605600-91607000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:91605800-91606600	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr10:91606000-91606600	Enhancers	NH-A	brain
18	chr10:91606000-91606800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr10:91606000-91606800	Enhancers	HepG2	liver
20	chr10:91606000-91607000	Enhancers	H9 Cell Line	embryonic stem cell
21	chr10:91606000-91607000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr10:91606200-91606600	Enhancers	Fetal Intestine Large	intestine
23	chr10:91606200-91607200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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