Variant report

Variant	rs7612463
Chromosome Location	chr3:23336450-23336451
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10428163	0.81[EUR][1000 genomes]
rs10510536	0.89[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11926494	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs11927173	0.87[ASN][1000 genomes]
rs13094957	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1495130	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1496653	0.94[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs17012800	0.89[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17012829	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17013266	1.00[CHB][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs1845899	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1908475	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs2017065	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2173058	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2359765	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs2359766	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs35352848	0.81[ASN][1000 genomes]
rs35901544	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4327332	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4340647	0.89[CEU][hapmap]
rs56979234	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57131555	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57625069	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58724157	0.86[ASN][1000 genomes]
rs59687869	0.81[ASN][1000 genomes]
rs60782093	0.87[ASN][1000 genomes]
rs61578857	0.87[ASN][1000 genomes]
rs6764347	0.81[AMR][1000 genomes]
rs6765801	0.87[ASN][1000 genomes]
rs6769167	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792370	1.00[ASW][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6808488	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73823472	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7612812	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7613185	0.89[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7627380	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7627525	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs7628372	0.89[CEU][hapmap];0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs7641437	0.89[CHB][hapmap]
rs9866739	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9867046	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9883870	0.89[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1004417	chr3:23318797-23389422	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Type 2 diabetes	24509480	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7612463	C3orf48	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23298800-23336600	Weak transcription	Thymus	Thymus
2	chr3:23329200-23336600	Weak transcription	Primary B cells from cord blood	blood
3	chr3:23334000-23336600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:23334400-23337000	Weak transcription	Psoas Muscle	Psoas
5	chr3:23336400-23336600	Active TSS	GM12878-XiMat	blood

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