Variant report

Variant	rs12075929
Chromosome Location	chr1:86248138-86248139
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10493773	0.92[CEU][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs10493774	0.92[CEU][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes]
rs11161649	0.96[CEU][hapmap]
rs12061951	0.81[ASW][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap]
rs12066742	0.83[JPT][hapmap]
rs12067749	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12564080	0.83[ASW][hapmap];0.96[CEU][hapmap];0.96[LWK][hapmap];0.82[MKK][hapmap]
rs12722770	0.83[AMR][1000 genomes]
rs12739713	0.96[CEU][hapmap]
rs12751296	0.85[AMR][1000 genomes]
rs12754358	0.88[CEU][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12756013	0.82[CEU][hapmap]
rs2069208	0.96[CEU][hapmap]
rs2274738	0.92[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs3753789	0.82[LWK][hapmap]
rs3767163	0.92[CEU][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs414618	0.88[CEU][hapmap]
rs55654440	0.85[AMR][1000 genomes]
rs6576784	0.96[CEU][hapmap]
rs6667672	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6689168	0.83[ASW][hapmap]
rs6697548	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6698578	0.91[CEU][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes]
rs7518312	0.81[AFR][1000 genomes]
rs7523292	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv546721	chr1:86226352-86392577	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv999743	chr1:86241246-86364846	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12075929	DNASE2B	cis	cerebellum	SCAN
rs12075929	C1orf52	cis	cerebellum	SCAN
rs12075929	ZNHIT6	cis	lymphoblastoid	seeQTL
rs12075929	RPF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86222400-86248200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:86222800-86254400	Weak transcription	Fetal Lung	lung
3	chr1:86239800-86253800	Weak transcription	GM12878-XiMat	blood
4	chr1:86244600-86251400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:86246200-86251000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:86246400-86249200	Strong transcription	Primary hematopoietic stem cells	blood

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