Variant report

Variant	rs9825100
Chromosome Location	chr3:139915713-139915714
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:139913497..139916210-chr3:139916643..139919277,2	K562	blood:
2	chr3:139915235..139917863-chr3:139919507..139921140,2	K562	blood:
3	chr3:139905931..139907924-chr3:139914336..139916960,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11706003	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[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]
rs11713717	0.81[ASN][1000 genomes]
rs12629075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35260142	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4305391	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4336075	0.86[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4361242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683810	0.86[CEU][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4683811	0.83[CHD][hapmap]
rs6767999	0.96[ASN][1000 genomes]
rs7612325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9810392	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]
rs9811727	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815878	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9818249	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9818563	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9818712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9822648	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9823347	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9856654	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap]
rs9876646	0.88[EUR][1000 genomes];0.96[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
rs9825100	CHST2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139909200-139917000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:139915200-139918000	Enhancers	Right Atrium	heart
3	chr3:139915200-139918400	Enhancers	Brain Anterior Caudate	brain
4	chr3:139915200-139920000	Enhancers	Brain Cingulate Gyrus	brain
5	chr3:139915400-139916000	Enhancers	Psoas Muscle	Psoas
6	chr3:139915400-139916400	Weak transcription	Brain Angular Gyrus	brain
7	chr3:139915400-139917000	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:139915400-139918600	Enhancers	Brain Hippocampus Middle	brain
9	chr3:139915600-139915800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:139915600-139916000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:139915600-139920400	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links