Variant report

Variant	rs10840404
Chromosome Location	chr11:10426129-10426130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10770111	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12574619	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12577015	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923084	0.83[CHB][hapmap]
rs35130571	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60472696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71476869	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs752373	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1037131	chr11:10401998-10429998	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv553477	chr11:10403539-10429998	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10840404	RPL27A	cis	cerebellum	SCAN
rs10840404	SCUBE2	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10414600-10427400	Weak transcription	Ovary	ovary
2	chr11:10415600-10436000	Weak transcription	Right Ventricle	heart
3	chr11:10417800-10427400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr11:10420400-10427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:10420400-10429400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:10420600-10427400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:10422200-10430800	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:10422800-10427600	Weak transcription	NHEK	skin
9	chr11:10422800-10427800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr11:10423000-10427400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:10423000-10427400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:10423000-10428200	Weak transcription	NH-A	brain
13	chr11:10423000-10428800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:10423000-10430400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:10423000-10430600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:10423200-10427200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:10423200-10427400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:10423200-10427600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:10423200-10428600	Weak transcription	Right Atrium	heart
20	chr11:10423200-10429200	Weak transcription	Lung	lung
21	chr11:10423400-10427200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:10423400-10427600	Weak transcription	HUVEC	blood vessel
23	chr11:10423400-10428600	Weak transcription	Brain Substantia Nigra	brain
24	chr11:10423600-10427600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:10423800-10427400	Weak transcription	Brain Hippocampus Middle	brain
26	chr11:10423800-10427400	Weak transcription	Psoas Muscle	Psoas
27	chr11:10423800-10428600	Weak transcription	Brain Anterior Caudate	brain
28	chr11:10423800-10430600	Weak transcription	Brain Angular Gyrus	brain
29	chr11:10424000-10427200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr11:10424000-10427200	Weak transcription	Adipose Nuclei	Adipose
31	chr11:10424000-10427400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr11:10424000-10428000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr11:10424200-10427200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:10424200-10427400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr11:10424200-10427600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:10424200-10427800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:10424200-10427800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr11:10424400-10427600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr11:10425000-10429000	Weak transcription	Placenta	Placenta
40	chr11:10425400-10427400	Weak transcription	Spleen	Spleen
41	chr11:10426000-10426400	Enhancers	NHDF-Ad	bronchial
42	chr11:10426000-10426800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:10426000-10428600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links