Variant report

Variant	rs12675153
Chromosome Location	chr8:10356187-10356188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:10354981..10356496-chr8:10377351..10379387,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12675653	0.87[CEU][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs12676059	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs12676436	0.87[CEU][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs12677569	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs12679191	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12681804	0.94[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs28378036	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28701524	0.87[EUR][1000 genomes]
rs4269499	0.89[EUR][1000 genomes]
rs4288337	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4294152	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4473996	0.89[EUR][1000 genomes]
rs4480076	0.87[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs4588813	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4840488	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4841359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56246075	0.87[EUR][1000 genomes]
rs58912510	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61094924	0.86[EUR][1000 genomes]
rs62492775	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62492779	0.87[EUR][1000 genomes]
rs62492782	0.86[EUR][1000 genomes]
rs6601471	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6989332	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6997045	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7009115	0.86[EUR][1000 genomes]
rs73195174	0.87[EUR][1000 genomes]
rs7387481	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9657517	0.87[CEU][hapmap];0.87[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	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
6	nsv610267	chr8:10268736-10526742	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1019090	chr8:10303099-10369061	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1024976	chr8:10303099-10385361	Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1030856	chr8:10303099-10439064	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv610268	chr8:10331636-10486652	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv1025251	chr8:10343591-10488557	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12675153	XKR6	cis	cerebellum	SCAN
rs12675153	PRSS55	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10335800-10357600	Weak transcription	Brain Anterior Caudate	brain
2	chr8:10338000-10357600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr8:10339600-10357600	Weak transcription	Liver	Liver
4	chr8:10355600-10358200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr8:10356000-10356400	Strong transcription	Brain Germinal Matrix	brain
6	chr8:10356000-10358000	Weak transcription	Fetal Brain Female	brain

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