Variant report

Variant	rs60740654
Chromosome Location	chr3:51324026-51324027
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12485331	0.84[EUR][1000 genomes]
rs12485754	0.84[EUR][1000 genomes]
rs12487468	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12487496	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12489219	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490026	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12491836	0.89[EUR][1000 genomes]
rs12492615	0.89[EUR][1000 genomes]
rs12492690	0.89[EUR][1000 genomes]
rs12493034	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493323	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493978	0.80[AMR][1000 genomes]
rs12495561	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496830	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1809388	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1842394	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2086395	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2101056	0.97[ASN][1000 genomes]
rs2127654	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2170177	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2355946	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762711	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4130473	0.89[EUR][1000 genomes]
rs4346580	0.89[EUR][1000 genomes]
rs4468966	0.85[AMR][1000 genomes]
rs4927961	0.89[EUR][1000 genomes]
rs4974100	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974112	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56052360	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57406588	0.89[EUR][1000 genomes]
rs58201844	0.85[AMR][1000 genomes]
rs58911602	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59129045	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59682667	0.89[EUR][1000 genomes]
rs59834534	0.89[EUR][1000 genomes]
rs60128296	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60461297	0.89[EUR][1000 genomes]
rs60567238	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61660900	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792254	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72936442	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72936462	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941919	0.89[EUR][1000 genomes]
rs72943166	0.89[EUR][1000 genomes]
rs72948197	0.89[EUR][1000 genomes]
rs72948200	0.89[EUR][1000 genomes]
rs72953143	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72953162	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72953175	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs751076	0.83[AMR][1000 genomes]
rs880478	0.83[AMR][1000 genomes]
rs9817077	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9817872	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9819195	0.85[AMR][1000 genomes]
rs9829057	0.85[AMR][1000 genomes]
rs9856134	0.85[AMR][1000 genomes]
rs9878592	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51315400-51350000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:51318200-51328600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:51318600-51324400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:51319600-51324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:51320000-51324200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:51321000-51324400	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:51321000-51324600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:51322600-51324600	Weak transcription	Brain Anterior Caudate	brain
9	chr3:51322600-51329000	Weak transcription	Brain Angular Gyrus	brain
10	chr3:51322800-51327800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:51323000-51325800	Weak transcription	Brain Germinal Matrix	brain
12	chr3:51323800-51324200	ZNF genes & repeats	Brain Hippocampus Middle	brain
13	chr3:51324000-51324600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links