Variant report

Variant	rs1397645
Chromosome Location	chr4:121957734-121957735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11931955	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11945593	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11946567	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13108974	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1397646	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775913	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456980	0.93[EUR][1000 genomes]
rs4605682	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56242650	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58294830	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58510164	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7690446	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3386870	chr4:121867625-122208448	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv879859	chr4:121892490-122438312	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription 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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1397645	SPATA5	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121952200-121979600	Weak transcription	Psoas Muscle	Psoas
2	chr4:121952400-121961400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:121953600-121968600	Weak transcription	NHDF-Ad	bronchial
4	chr4:121954000-121957800	Weak transcription	Lung	lung
5	chr4:121954000-121962800	Weak transcription	Left Ventricle	heart
6	chr4:121955600-121967000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:121956000-121959200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:121956000-121959200	Weak transcription	Brain Substantia Nigra	brain
9	chr4:121956200-121957800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:121956600-121958200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:121957200-121959000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:121957200-121959400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:121957200-121959400	Strong transcription	Fetal Lung	lung
14	chr4:121957200-121963200	Strong transcription	Fetal Intestine Large	intestine
15	chr4:121957400-121958400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:121957400-121962400	Weak transcription	Fetal Kidney	kidney
17	chr4:121957400-121963200	Strong transcription	Ovary	ovary
18	chr4:121957600-121958600	Strong transcription	Adipose Nuclei	Adipose
19	chr4:121957600-121958800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:121957600-121958800	Strong transcription	Fetal Intestine Small	intestine

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