Variant report

Variant	rs9289849
Chromosome Location	chr3:151254152-151254153
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	chr3:151253397..151255713-chr3:151264591..151266186,2	MCF-7	breast:
2	chr3:151252320..151254968-chr3:151257650..151259155,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10935861	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11712630	0.82[EUR][1000 genomes]
rs12630095	0.96[CEU][hapmap]
rs12634284	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12639049	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4128734	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4345047	0.83[EUR][1000 genomes]
rs4381913	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4608665	0.82[EUR][1000 genomes]
rs4679836	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs4679837	0.89[CEU][hapmap];0.87[JPT][hapmap]
rs4680465	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4680501	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440763	0.83[EUR][1000 genomes]
rs6798066	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6805953	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7375135	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7427312	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617486	0.82[EUR][1000 genomes]
rs7617799	0.82[EUR][1000 genomes]
rs7625809	0.80[AMR][1000 genomes]
rs7629172	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7629867	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7629912	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7636304	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7637619	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7647576	0.85[EUR][1000 genomes]
rs9289847	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9680970	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9683349	0.85[EUR][1000 genomes]
rs9811565	0.82[EUR][1000 genomes]
rs9817125	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9822315	0.82[EUR][1000 genomes]
rs9830648	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9836445	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846323	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9849929	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9850195	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995048	chr3:151114074-151560019	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv877650	chr3:151174010-151314449	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9289849	GMPS	cis	cerebellum	SCAN
rs9289849	IGSF10	cis	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151253600-151254400	Enhancers	Fetal Lung	lung
2	chr3:151253800-151254200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:151253800-151254400	Enhancers	H9 Cell Line	embryonic stem cell
4	chr3:151254000-151254200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:151254000-151254200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:151254000-151254200	Flanking Active TSS	Ovary	ovary
7	chr3:151254000-151255600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:151254000-151256600	Weak transcription	Psoas Muscle	Psoas
9	chr3:151254000-151257000	Weak transcription	Fetal Stomach	stomach

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