Variant report

Variant	rs10090444
Chromosome Location	chr8:10745469-10745470
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10089518	1.00[CHB][hapmap]
rs10096381	0.81[CEU][hapmap]
rs10107145	0.96[CEU][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10903337	1.00[CHB][hapmap]
rs11250084	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs11250092	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs11250093	0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs11250094	0.87[CEU][hapmap]
rs11250099	0.81[CEU][hapmap]
rs11783247	0.89[CEU][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs12542037	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs12546366	0.85[CEU][hapmap];0.85[MEX][hapmap]
rs13248264	1.00[CHB][hapmap]
rs13248287	1.00[JPT][hapmap]
rs13248300	1.00[CHB][hapmap]
rs13251528	1.00[CHB][hapmap]
rs13279922	1.00[JPT][hapmap]
rs1430866	1.00[JPT][hapmap]
rs1529598	1.00[JPT][hapmap]
rs17152841	1.00[CHB][hapmap]
rs17778581	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17779791	1.00[CHB][hapmap]
rs2409691	1.00[CHB][hapmap]
rs2409692	1.00[CHB][hapmap]
rs2409693	1.00[CHB][hapmap]
rs34741518	0.84[EUR][1000 genomes]
rs4240671	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs4240672	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4240673	0.92[CEU][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs4326350	1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs4841457	0.85[EUR][1000 genomes]
rs4841460	1.00[CHB][hapmap]
rs4841486	1.00[CHB][hapmap]
rs6601544	0.81[CEU][hapmap]
rs6984496	0.92[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap]
rs6985109	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6996943	0.84[CEU][hapmap]
rs7016385	0.89[CEU][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs755856	0.87[AFR][1000 genomes]
rs7813037	1.00[JPT][hapmap]
rs7821826	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7823296	0.84[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7843666	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9657544	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1026802	chr8:10576444-10754489	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv539469	chr8:10576444-10754489	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv831232	chr8:10606053-10774948	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1031726	chr8:10627742-10749369	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv508497	chr8:10680621-10750255	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10090444	CTSB	cis	cerebellum	SCAN
rs10090444	PRSS55	cis	cerebellum	SCAN
rs10090444	FAM167A	cis	lymphoblastoid	seeQTL
rs10090444	MFHAS1	cis	cerebellum	SCAN
rs10090444	CLDN23	cis	multi-tissue	Pritchard
rs10090444	TDH	cis	cerebellum	SCAN
rs10090444	DEFB134	cis	cerebellum	SCAN
rs10090444	DEFB134	cis	parietal	SCAN
rs10090444	C8orf13	cis	multi-tissue	Pritchard
rs10090444	DEFB136	cis	parietal	SCAN
rs10090444	FLJ10661	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10720800-10756200	Weak transcription	Pancreas	Pancrea
2	chr8:10743800-10750000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:10744800-10745600	Enhancers	Dnd41	blood
4	chr8:10745200-10745600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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