Variant report

Variant	rs4240673
Chromosome Location	chr8:10787612-10787613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10090444	0.82[EUR][1000 genomes]
rs10096381	0.81[CEU][hapmap]
rs10107145	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs10110723	1.00[JPT][hapmap]
rs11250092	0.96[CEU][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11250093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11250094	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11250099	0.81[CEU][hapmap]
rs11776368	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11777007	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11783247	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11783749	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11990550	1.00[CHB][hapmap]
rs11993591	1.00[CHB][hapmap]
rs12542037	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12546366	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap]
rs12548184	0.81[AMR][1000 genomes]
rs2409692	1.00[CHB][hapmap]
rs34741518	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073948	0.85[EUR][1000 genomes]
rs4240671	0.81[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs4326350	0.90[MEX][hapmap];0.89[TSI][hapmap]
rs4520127	1.00[CHB][hapmap]
rs4554431	0.83[ASN][1000 genomes]
rs4841457	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841458	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4841460	1.00[CHB][hapmap]
rs4841461	1.00[JPT][hapmap]
rs4841465	0.85[CEU][hapmap]
rs6601544	0.81[CEU][hapmap]
rs6984496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6985109	0.96[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs6988281	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6992103	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6996943	0.83[CEU][hapmap]
rs7005884	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7015168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7016385	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7823296	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7833435	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7837038	1.00[CHB][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs7843470	0.81[CEU][hapmap]

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	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1017836	chr8:10591801-10803617	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1034988	chr8:10591801-10804243	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1025190	chr8:10756331-10802566	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4240673	CTSB	cis	cerebellum	SCAN
rs4240673	MFHAS1	cis	cerebellum	SCAN
rs4240673	C8orf13	Cis_1M	lymphoblastoid	RTeQTL
rs4240673	DEFB134	cis	cerebellum	SCAN
rs4240673	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs4240673	TDH	cis	cerebellum	SCAN
rs4240673	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs4240673	DEFB136	cis	parietal	SCAN
rs4240673	FLJ10661	cis	cerebellum	SCAN
rs4240673	PRSS55	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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