Variant report

Variant	rs9804260
Chromosome Location	chr10:117980452-117980453
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:117980062..117982320-chr10:117983551..117985894,2	MCF-7	breast:
2	chr10:117918621..117920371-chr10:117978325..117980983,2	MCF-7	breast:
3	chr10:117979962..117982237-chr10:118008669..118010645,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10430632	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10749203	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10787637	0.90[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1079261	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10885876	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10885877	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10885878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11197582	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11197585	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2901063	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3781551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4259753	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4269847	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4356140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4384313	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4550150	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4611119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7090693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7096877	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7096912	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs881042	0.94[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs881726	0.82[GIH][hapmap];0.80[TSI][hapmap]
rs9731211	0.96[EUR][1000 genomes];0.93[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	esv3449389	chr10:117806874-118102404	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832000	chr10:117944492-118116253	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9804260	C10orf84	cis	cerebellum	SCAN
rs9804260	PNLIPRP2	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:117973400-117986400	Weak transcription	Fetal Stomach	stomach
2	chr10:117973600-117989200	Weak transcription	HSMMtube	muscle
3	chr10:117975600-117987600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr10:117976800-117999800	Weak transcription	HSMM	muscle
5	chr10:117978200-117995600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:117979400-117982400	Enhancers	Liver	Liver
7	chr10:117980000-117981400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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