Variant report

Variant	rs6601542
Chromosome Location	chr8:10832865-10832866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10093514	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10096421	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.99[ASN][1000 genomes]
rs28494533	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34959618	0.86[EUR][1000 genomes]
rs3885690	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4078189	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4841466	0.97[ASN][1000 genomes]
rs4841467	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6601541	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6983869	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7013277	0.84[CEU][hapmap];0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6601542	MFHAS1	cis	cerebellum	SCAN
rs6601542	AF131215.2	cis	Nerve Tibial	GTEx
rs6601542	TDH	cis	cerebellum	SCAN
rs6601542	DEFB134	cis	cerebellum	SCAN
rs6601542	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs6601542	PRSS55	cis	cerebellum	SCAN
rs6601542	FLJ10661	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10830200-10836200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:10830200-10836400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr8:10832600-10833200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:10832800-10833000	Enhancers	Spleen	Spleen

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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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