Variant report

Variant	rs12496830
Chromosome Location	chr3:51292163-51292164
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12485331	0.84[EUR][1000 genomes]
rs12485754	0.84[EUR][1000 genomes]
rs12487496	0.89[EUR][1000 genomes]
rs12489219	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490026	0.89[EUR][1000 genomes]
rs12491836	0.89[EUR][1000 genomes]
rs12492615	0.89[EUR][1000 genomes]
rs12492690	0.89[EUR][1000 genomes]
rs12493034	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493323	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12495561	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1809388	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2086395	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2101056	0.93[ASN][1000 genomes]
rs2127654	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2170177	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2355946	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3762711	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4130473	0.89[EUR][1000 genomes]
rs4346580	0.89[EUR][1000 genomes]
rs4927961	0.89[EUR][1000 genomes]
rs4974100	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4974112	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56052360	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57406588	0.89[EUR][1000 genomes]
rs58911602	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59129045	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59682667	0.89[EUR][1000 genomes]
rs59834534	0.89[EUR][1000 genomes]
rs60128296	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60461297	0.89[EUR][1000 genomes]
rs60567238	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60740654	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61578076	0.84[AFR][1000 genomes]
rs61660900	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792254	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72936442	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72936462	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[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	0.89[EUR][1000 genomes]
rs72953162	0.89[EUR][1000 genomes]
rs72953175	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9878592	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51252000-51312600	Weak transcription	HSMMtube	muscle
2	chr3:51253400-51312200	Weak transcription	Brain Substantia Nigra	brain
3	chr3:51266400-51297000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:51267000-51297600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:51268000-51296200	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:51280400-51298800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:51285400-51308200	Weak transcription	Brain Anterior Caudate	brain
8	chr3:51285600-51294200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:51285600-51297600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:51285600-51298000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:51285800-51297400	Weak transcription	Brain Germinal Matrix	brain
12	chr3:51285800-51297600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:51288200-51319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:51289000-51298800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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