Variant report

Variant	rs1530477
Chromosome Location	chr3:143819506-143819507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1025984	0.83[GIH][hapmap]
rs13068298	0.85[CEU][hapmap]
rs13091882	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1466941	0.83[GIH][hapmap]
rs1530478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530479	0.82[EUR][1000 genomes]
rs17602500	0.86[GIH][hapmap]
rs17667256	0.83[GIH][hapmap]
rs1898265	0.80[EUR][1000 genomes]
rs1992093	0.86[GIH][hapmap]
rs34379944	0.81[EUR][1000 genomes]
rs34639473	0.83[EUR][1000 genomes]
rs34730687	0.83[EUR][1000 genomes]
rs35885310	0.80[EUR][1000 genomes]
rs56196484	0.81[EUR][1000 genomes]
rs62269933	0.83[EUR][1000 genomes]
rs6440210	0.83[GIH][hapmap]
rs6767236	0.95[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs6782024	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784938	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786460	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6804060	0.90[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs721572	0.86[GIH][hapmap]
rs7621079	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621093	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7653331	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs951865	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs989665	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1010117	chr3:143750590-144093775	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv536748	chr3:143750590-144093775	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv877569	chr3:143762420-143825439	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1010213	chr3:143775358-143863149	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv591923	chr3:143776096-143862350	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv591924	chr3:143776096-143864780	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1008414	chr3:143779087-143853396	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1009018	chr3:143797683-143868350	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv532633	chr3:143802417-144440646	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1530477	C3orf58	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143809600-143821200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:143817600-143819800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:143818600-143824000	Weak transcription	Ovary	ovary
4	chr3:143819000-143821000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:143819000-143823000	Weak transcription	Liver	Liver
6	chr3:143819200-143823000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:143819200-143823000	Weak transcription	Aorta	Aorta
8	chr3:143819200-143824400	Weak transcription	Pancreas	Pancrea
9	chr3:143819400-143821200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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