Variant report

Variant	rs9810392
Chromosome Location	chr3:139907483-139907484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:139907221..139909210-chr3:139909774..139912036,2	MCF-7	breast:
2	chr3:139905931..139907924-chr3:139914336..139916960,2	K562	blood:
3	chr3:139901794..139903880-chr3:139906327..139907878,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11706003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707235	0.81[CHD][hapmap]
rs11713717	0.88[ASN][1000 genomes]
rs12629075	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17402510	0.81[CHD][hapmap]
rs35260142	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4305391	0.87[CEU][hapmap];0.89[GIH][hapmap];0.80[ASN][1000 genomes]
rs4336075	0.91[GIH][hapmap];0.80[ASN][1000 genomes]
rs4361242	0.82[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4532091	0.81[CHD][hapmap]
rs4683810	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6767999	0.92[ASN][1000 genomes]
rs6808021	0.81[CHD][hapmap]
rs7612325	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9811727	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9815072	0.81[CHD][hapmap]
rs9815878	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9816340	0.81[CHD][hapmap]
rs9818249	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9818563	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9818712	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9822648	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9823347	0.87[CEU][hapmap];0.89[GIH][hapmap];0.80[ASN][1000 genomes]
rs9825100	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9856654	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9876646	0.90[EUR][1000 genomes];0.92[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	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv829739	chr3:139797496-140002685	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1008578	chr3:139907172-139942453	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1003141	chr3:139907434-139942453	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9810392	CHST2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139901600-139915000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:139903400-139907600	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr3:139903600-139908000	Enhancers	Fetal Heart	heart
4	chr3:139905000-139908000	Enhancers	Brain Germinal Matrix	brain
5	chr3:139905200-139908000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:139905800-139907600	Enhancers	Left Ventricle	heart
7	chr3:139905800-139907800	Enhancers	Right Ventricle	heart
8	chr3:139906400-139913000	Weak transcription	HSMMtube	muscle
9	chr3:139907400-139908600	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:139907400-139908800	Weak transcription	Psoas Muscle	Psoas

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