Variant report

Variant	rs12485754
Chromosome Location	chr3:51141414-51141415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12485331	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487496	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12489219	0.84[EUR][1000 genomes]
rs12490026	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12491836	0.95[EUR][1000 genomes]
rs12492615	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12492690	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12493034	0.84[EUR][1000 genomes]
rs12493323	0.84[EUR][1000 genomes]
rs12493359	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12495561	0.84[EUR][1000 genomes]
rs12496830	0.84[EUR][1000 genomes]
rs1809388	0.84[EUR][1000 genomes]
rs2086395	0.84[EUR][1000 genomes]
rs2127654	0.95[EUR][1000 genomes]
rs3762711	0.95[EUR][1000 genomes]
rs4130473	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4323036	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4346580	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4927961	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4974100	0.84[EUR][1000 genomes]
rs4974112	0.84[EUR][1000 genomes]
rs56052360	0.84[EUR][1000 genomes]
rs57406588	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58720544	0.84[EUR][1000 genomes]
rs58911602	0.84[EUR][1000 genomes]
rs59682667	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59834534	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59957657	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60461297	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60567238	0.84[EUR][1000 genomes]
rs60740654	0.84[EUR][1000 genomes]
rs60882641	0.84[EUR][1000 genomes]
rs6792254	0.84[EUR][1000 genomes]
rs72936442	0.84[EUR][1000 genomes]
rs72941919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72943130	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72943137	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72943166	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72948197	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72948200	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72953143	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72953162	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72953175	0.95[EUR][1000 genomes]
rs7372342	0.84[EUR][1000 genomes]
rs9878592	0.84[EUR][1000 genomes]

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	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv3447639	chr3:51129523-51158383	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51120800-51143000	Weak transcription	Brain Angular Gyrus	brain
2	chr3:51121000-51143000	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:51121000-51145200	Weak transcription	Fetal Brain Male	brain
4	chr3:51122000-51143000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:51122800-51143000	Weak transcription	Fetal Brain Female	brain
6	chr3:51124200-51143000	Weak transcription	Brain Germinal Matrix	brain
7	chr3:51125400-51143000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:51125400-51143200	Weak transcription	Brain Substantia Nigra	brain
9	chr3:51128200-51143800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:51128400-51142800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:51129600-51143200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:51129800-51143600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:51132600-51143800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:51135000-51143800	Weak transcription	Brain Anterior Caudate	brain
15	chr3:51135600-51142600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:51137800-51142200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:51137800-51143000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:51137800-51143200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:51141200-51142000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr3:51141400-51141600	Enhancers	Stomach Smooth Muscle	stomach

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