Variant report

Variant	rs7653648
Chromosome Location	chr3:54407202-54407203
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11709302	0.89[EUR][1000 genomes]
rs11711662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13082754	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs1375521	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1375522	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1449331	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1473348	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1992963	0.82[GIH][hapmap]
rs1992964	0.82[GIH][hapmap]
rs2359785	0.90[EUR][1000 genomes]
rs2359786	0.87[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs2359790	0.82[TSI][hapmap]
rs2359793	0.82[TSI][hapmap]
rs4131315	0.82[GIH][hapmap]
rs6445653	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs6445655	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs6445657	0.84[EUR][1000 genomes]
rs6769553	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs6777368	0.84[EUR][1000 genomes]
rs6804196	0.87[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap]
rs731508	0.87[CEU][hapmap];0.90[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs7372585	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7374435	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs7426795	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7429237	0.82[GIH][hapmap]
rs7645545	0.88[CEU][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs9817603	0.87[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap]
rs9826277	0.87[CEU][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes]
rs9843412	0.87[CEU][hapmap];0.90[CHB][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs9864105	0.88[CEU][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs9874831	0.87[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7653648	DNASE1L3	cis	parietal	SCAN
rs7653648	TKT	cis	parietal	SCAN
rs7653648	SEMA3G	cis	parietal	SCAN
rs7653648	HESX1	cis	cerebellum	SCAN
rs7653648	RBM15B	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54392600-54410200	Weak transcription	Ovary	ovary
2	chr3:54395400-54407800	Weak transcription	Hela-S3	cervix
3	chr3:54395400-54409000	Weak transcription	Right Atrium	heart
4	chr3:54401000-54409600	Weak transcription	Fetal Lung	lung
5	chr3:54406400-54410200	Weak transcription	Psoas Muscle	Psoas
6	chr3:54407000-54408000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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