Variant report

Variant	rs9878902
Chromosome Location	chr3:144220319-144220320
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153580940..153582973-chr3:144219455..144221982,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188643	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10935507	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11928775	0.96[ASN][1000 genomes]
rs12490144	0.88[ASN][1000 genomes]
rs12491851	0.96[ASN][1000 genomes]
rs12493075	0.96[ASN][1000 genomes]
rs12494918	0.92[ASN][1000 genomes]
rs12495279	0.96[ASN][1000 genomes]
rs13066453	1.00[ASN][1000 genomes]
rs1527238	1.00[ASN][1000 genomes]
rs1529752	0.94[ASN][1000 genomes]
rs1529753	0.94[ASN][1000 genomes]
rs1657010	0.88[EUR][1000 genomes]
rs1726522	0.86[ASN][1000 genomes]
rs1726536	0.84[ASN][1000 genomes]
rs1726538	0.84[ASN][1000 genomes]
rs2117004	0.92[ASN][1000 genomes]
rs2222702	0.83[ASN][1000 genomes]
rs2575189	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2694959	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2717380	0.83[ASN][1000 genomes]
rs2717387	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2717388	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2717389	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34130084	0.89[EUR][1000 genomes]
rs4337676	0.98[ASN][1000 genomes]
rs4349542	0.89[ASN][1000 genomes]
rs4398472	0.98[ASN][1000 genomes]
rs4408907	0.98[ASN][1000 genomes]
rs4479640	1.00[ASN][1000 genomes]
rs4544660	0.98[ASN][1000 genomes]
rs4568182	0.98[ASN][1000 genomes]
rs4594657	0.98[ASN][1000 genomes]
rs4681125	1.00[ASN][1000 genomes]
rs4681126	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681328	0.97[ASN][1000 genomes]
rs4681331	0.98[ASN][1000 genomes]
rs4681342	1.00[ASN][1000 genomes]
rs6440258	0.99[ASN][1000 genomes]
rs6763327	0.96[ASN][1000 genomes]
rs6763662	0.96[ASN][1000 genomes]
rs6783056	0.89[ASN][1000 genomes]
rs6791653	0.92[ASN][1000 genomes]
rs6799623	0.99[ASN][1000 genomes]
rs6800761	0.98[ASN][1000 genomes]
rs721029	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs721030	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7611785	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7613977	0.98[ASN][1000 genomes]
rs7614082	0.92[ASN][1000 genomes]
rs7614253	0.89[ASN][1000 genomes]
rs7615146	0.99[ASN][1000 genomes]
rs7616429	1.00[ASN][1000 genomes]
rs7620611	0.98[ASN][1000 genomes]
rs7626294	0.95[ASN][1000 genomes]
rs7628103	0.98[ASN][1000 genomes]
rs7634647	1.00[ASN][1000 genomes]
rs7637942	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7648433	0.96[ASN][1000 genomes]
rs7650699	0.98[ASN][1000 genomes]
rs7652161	0.96[ASN][1000 genomes]
rs7653820	0.99[ASN][1000 genomes]
rs9829827	0.92[ASN][1000 genomes]
rs9833354	0.99[ASN][1000 genomes]
rs9840395	0.95[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9844730	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9857163	0.96[ASN][1000 genomes]
rs9857613	0.96[ASN][1000 genomes]
rs9866115	0.96[ASN][1000 genomes]
rs9866198	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9866442	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9870285	0.86[ASN][1000 genomes]
rs9873732	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532633	chr3:143802417-144440646	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591928	chr3:144050897-144822081	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2756108	chr3:144177836-144301659	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877571	chr3:144188561-144291254	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9878902	PLSCR1	cis	cerebellum	SCAN
rs9878902	COMMD2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:144215600-144220400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:144216400-144221000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:144216600-144221000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:144218600-144220400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:144219400-144220400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:144219600-144221600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:144220200-144221200	Enhancers	Primary hematopoietic stem cells	blood
8	chr3:144220200-144221400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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