Variant report

Variant	rs12408760
Chromosome Location	chr1:209749159-209749160
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209749002..209750989-chr1:209793739..209796003,2	MCF-7	breast:
2	chr1:209749053..209751120-chr1:209781399..209783226,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11119313	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs11801272	0.84[EUR][1000 genomes]
rs12078982	0.86[ASN][1000 genomes]
rs12079523	0.85[ASN][1000 genomes]
rs12402938	0.88[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12734177	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2003681	0.81[ASN][1000 genomes]
rs2015617	0.86[ASN][1000 genomes]
rs2235449	0.84[EUR][1000 genomes]
rs2235452	0.88[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs2235453	0.88[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs2235454	0.84[EUR][1000 genomes]
rs2235455	0.84[EUR][1000 genomes]
rs2356933	0.87[CHB][hapmap]
rs35104617	0.87[EUR][1000 genomes]
rs35498535	0.84[EUR][1000 genomes]
rs35503098	0.87[EUR][1000 genomes]
rs35508847	0.84[EUR][1000 genomes]
rs35553417	0.89[EUR][1000 genomes]
rs4436393	0.86[ASN][1000 genomes]
rs4556360	0.87[CHB][hapmap]
rs55814069	0.86[EUR][1000 genomes]
rs56209412	0.86[ASN][1000 genomes]
rs6540544	0.83[CHB][hapmap]
rs6695896	0.83[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs713074	0.87[CHB][hapmap]
rs7517804	0.86[EUR][1000 genomes]
rs7517839	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs7522730	0.87[CHB][hapmap]
rs7525534	0.84[ASN][1000 genomes]
rs7528476	0.87[CHB][hapmap]
rs7533785	0.95[CHB][hapmap]
rs7541174	0.86[ASN][1000 genomes]
rs7553120	0.83[EUR][1000 genomes]
rs760832	0.81[CHB][hapmap]
rs760833	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs926386	0.87[CHB][hapmap]
rs9430004	0.95[CHB][hapmap]
rs977441	0.87[CHB][hapmap]
rs9787069	0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12408760	HHAT	cis	parietal	SCAN
rs12408760	CDK18	cis	parietal	SCAN
rs12408760	SETD1A	trans	parietal	SCAN
rs12408760	PLXNA2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209744000-209750200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:209748400-209749400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:209748600-209750200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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