Variant report

Variant	rs9322089
Chromosome Location	chr6:147404954-147404955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:147400723..147405346-chr6:147522959..147527467,8	MCF-7	breast:
2	chr6:147385371..147387733-chr6:147404798..147406908,2	K562	blood:
3	chr6:147403737..147405712-chr6:147415493..147417404,3	K562	blood:

Variant related genes	Relation type
ENSG00000164506	Chromatin interaction
ENSG00000233452	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1105441	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12209736	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881660	0.81[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2256216	0.83[MEX][hapmap]
rs2328803	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3734477	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896903	0.84[EUR][1000 genomes]
rs6570788	0.84[AMR][1000 genomes]
rs6570789	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6901138	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6910250	0.92[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6920096	0.87[EUR][1000 genomes]
rs6920901	0.85[CHD][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs6924131	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6930740	0.94[ASW][hapmap];0.92[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7749744	1.00[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7755338	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7767185	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9322088	0.92[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9322090	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9377043	0.84[EUR][1000 genomes]
rs9377044	0.84[AMR][1000 genomes]
rs9377045	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9386178	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9403845	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9485141	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9497685	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9497690	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019245	chr6:147350834-147609776	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538467	chr6:147350834-147609776	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886751	chr6:147354092-147490398	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9322089	LTV1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147402600-147412000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:147403200-147408400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:147403800-147410000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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