Variant report

Variant	rs10061771
Chromosome Location	chr5:106916625-106916626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10045552	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479400	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479401	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153493	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12654557	0.95[ASN][1000 genomes]
rs12719573	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17348530	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1990993	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2005103	1.00[CHB][hapmap]
rs2406374	0.91[ASN][1000 genomes]
rs34052514	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34273069	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34644687	0.95[ASN][1000 genomes]
rs34950197	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864269	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4145099	0.86[GIH][hapmap]
rs4957704	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs597083	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62355632	0.91[ASN][1000 genomes]
rs62355633	0.91[ASN][1000 genomes]
rs641406	0.87[CHD][hapmap]
rs6888055	0.87[CHD][hapmap]
rs6894162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872240	1.00[CHB][hapmap];1.00[CHD][hapmap]

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	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10061771	EFNA5	cis	lymphoblastoid	seeQTL
rs10061771	ELK3	trans	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106908800-106917000	Weak transcription	HSMM	muscle
2	chr5:106908800-106917600	Enhancers	A549	lung
3	chr5:106909000-106917000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:106912200-106917600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:106913400-106916800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:106913600-106916800	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:106913600-106917000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:106913600-106917200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:106913600-106928800	Weak transcription	Right Ventricle	heart
10	chr5:106913800-106916800	Weak transcription	Fetal Stomach	stomach
11	chr5:106913800-106917000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:106913800-106924000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:106914000-106916800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:106914000-106916800	Weak transcription	Fetal Heart	heart
15	chr5:106914000-106917000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:106914000-106917200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:106914000-106924800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:106914200-106917000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:106914200-106924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:106914600-106919200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:106914800-106916800	Weak transcription	NHEK	skin
22	chr5:106914800-106928200	Weak transcription	Left Ventricle	heart
23	chr5:106915000-106916800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:106915000-106916800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:106915000-106917000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:106915000-106917000	Weak transcription	Adipose Nuclei	Adipose
27	chr5:106915000-106917000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:106915000-106917000	Weak transcription	GM12878-XiMat	blood
29	chr5:106915200-106929800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:106915400-106916800	Weak transcription	Fetal Kidney	kidney
31	chr5:106915600-106928200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:106916400-106917200	Enhancers	NHDF-Ad	bronchial
33	chr5:106916400-106917400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:106916400-106917600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:106916600-106917000	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr5:106916600-106917000	Enhancers	HMEC	breast
37	chr5:106916600-106917200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:106916600-106917400	Enhancers	Placenta Amnion	Placenta Amnion
39	chr5:106916600-106917400	Enhancers	Osteobl	bone
40	chr5:106916600-106917600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr5:106916600-106917600	Enhancers	Fetal Lung	lung
42	chr5:106916600-106918200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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