Variant report

Variant	rs12754358
Chromosome Location	chr1:86248431-86248432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10493773	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10493774	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11161649	0.84[CEU][hapmap]
rs12061951	0.84[YRI][hapmap]
rs12067749	0.83[AMR][1000 genomes]
rs12075929	0.88[CEU][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12564080	0.84[CEU][hapmap]
rs12722770	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12739713	0.84[CEU][hapmap]
rs12751296	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17398175	1.00[ASW][hapmap];0.85[CHD][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs2069208	0.84[CEU][hapmap]
rs2274738	0.96[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3767163	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55654440	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6576784	0.84[CEU][hapmap]
rs6667672	0.83[AMR][1000 genomes]
rs6697548	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6698578	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7523292	0.95[AMR][1000 genomes];0.81[ASN][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12754358	LOC339524	cis	parietal	SCAN
rs12754358	C1orf52	cis	cerebellum	SCAN
rs12754358	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs12754358	ZNHIT6	cis	lymphoblastoid	seeQTL
rs12754358	DNASE2B	cis	cerebellum	SCAN

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

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links