Variant report

Variant	rs12546366
Chromosome Location	chr8:10802146-10802147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10107145	0.88[CEU][hapmap]
rs10108618	0.81[MEX][hapmap]
rs11250092	0.89[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11250093	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11250094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11250099	0.81[CEU][hapmap]
rs11776368	1.00[CHB][hapmap]
rs11777007	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11783247	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap]
rs11783749	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11990550	1.00[CHB][hapmap]
rs11993591	1.00[CHB][hapmap]
rs12542037	0.84[CEU][hapmap]
rs12679529	0.80[EUR][1000 genomes]
rs2409691	0.81[MEX][hapmap]
rs2409692	1.00[CHB][hapmap]
rs34741518	0.81[EUR][1000 genomes]
rs35077714	0.83[ASN][1000 genomes]
rs4240671	0.81[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs4240673	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]
rs4326350	0.85[MEX][hapmap];0.80[TSI][hapmap]
rs4520127	1.00[CHB][hapmap]
rs4841457	0.81[EUR][1000 genomes]
rs4841458	1.00[CHB][hapmap]
rs4841460	1.00[CHB][hapmap]
rs4841461	0.82[JPT][hapmap]
rs4841465	0.85[CEU][hapmap]
rs6601564	0.80[MEX][hapmap]
rs6984496	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6985109	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs6988281	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6992103	1.00[CHB][hapmap]
rs7005884	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7015168	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7016385	0.90[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7823296	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7833435	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7837038	1.00[CHB][hapmap]
rs9657519	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv522127	chr8:10797831-10815515	Weak transcription Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv521721	chr8:10802102-10836472	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12546366	DEFB136	cis	parietal	SCAN
rs12546366	CTSB	cis	cerebellum	SCAN
rs12546366	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs12546366	MFHAS1	cis	cerebellum	SCAN
rs12546366	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs12546366	TDH	cis	cerebellum	SCAN
rs12546366	DEFB134	cis	cerebellum	SCAN
rs12546366	PRSS55	cis	cerebellum	SCAN
rs12546366	FLJ10661	cis	cerebellum	SCAN
rs12546366	C8orf48	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10795800-10805800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr8:10797600-10807200	Weak transcription	Right Atrium	heart
3	chr8:10800600-10803400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:10801600-10802600	Enhancers	Fetal Muscle Leg	muscle
5	chr8:10801600-10802800	Enhancers	Fetal Heart	heart
6	chr8:10801800-10802400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:10801800-10802600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:10801800-10802600	Enhancers	HSMMtube	muscle
9	chr8:10801800-10802800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr8:10801800-10802800	Enhancers	Fetal Muscle Trunk	muscle
11	chr8:10802000-10802400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr8:10802000-10802400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr8:10802000-10802600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr8:10802000-10802600	Enhancers	Right Ventricle	heart
15	chr8:10802000-10802800	Enhancers	Left Ventricle	heart

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