Variant report

Variant	rs1015629
Chromosome Location	chr7:83846895-83846896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10081337	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10085599	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10231889	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10233152	0.94[EUR][1000 genomes]
rs10260152	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10263842	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10265795	0.89[AFR][1000 genomes]
rs11971807	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11979170	0.94[JPT][hapmap]
rs12539919	0.95[JPT][hapmap]
rs1808204	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1989963	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2018407	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2214503	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2372167	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4607535	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs471152	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs471477	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs488333	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs489440	0.82[ASN][1000 genomes]
rs512896	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs514083	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs521401	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs537358	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs562475	0.82[ASN][1000 genomes]
rs569493	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs584566	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs589077	0.82[ASN][1000 genomes]
rs592778	0.82[ASN][1000 genomes]
rs600346	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs614046	0.82[ASN][1000 genomes]
rs645226	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs671711	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6946162	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6964607	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6969121	0.84[ASN][1000 genomes]
rs726978	0.82[ASN][1000 genomes]
rs727784	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7780987	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7782557	0.80[EUR][1000 genomes]
rs7787024	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7794860	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7799452	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7800664	0.80[EUR][1000 genomes]
rs7800995	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7805512	0.80[EUR][1000 genomes]
rs811622	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs812780	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs929275	0.83[EUR][1000 genomes]
rs9642175	0.95[JPT][hapmap]
rs996033	0.94[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv888629	chr7:83722691-83896025	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1017884	chr7:83724138-83972995	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538995	chr7:83724138-83972995	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1015629	KIAA1324L	cis	cerebellum	SCAN
rs1015629	GNAI1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83845800-83847200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr7:83846200-83847000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr7:83846200-83848600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:83846400-83847200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr7:83846600-83848000	Weak transcription	Fetal Heart	heart
6	chr7:83846800-83849000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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