Variant report

Variant	rs12339700
Chromosome Location	chr9:98117968-98117969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98081819..98084484-chr9:98117937..98119790,2	MCF-7	breast:
2	chr9:98103117..98105950-chr9:98116720..98118774,2	MCF-7	breast:
3	chr9:98112082..98114768-chr9:98116884..98119446,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10283758	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs10993503	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10993520	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1105979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337959	0.87[CEU][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12338907	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs12341302	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12342782	0.81[AMR][1000 genomes]
rs12350646	0.88[CEU][hapmap]
rs12352586	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs1886992	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28658564	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4237226	0.83[AMR][1000 genomes]
rs4647372	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4647373	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4647401	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4647404	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4647421	0.87[CEU][hapmap];0.84[AMR][1000 genomes]
rs4647432	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs4647441	0.83[AMR][1000 genomes]
rs4744445	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs4744453	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4744456	0.87[EUR][1000 genomes]
rs4744457	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4744458	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744460	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56134407	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62560523	0.84[AMR][1000 genomes]
rs7357617	0.87[CEU][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][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	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1045479	chr9:98115290-98172995	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98112200-98125400	Weak transcription	Gastric	stomach
2	chr9:98112400-98125400	Weak transcription	Pancreas	Pancrea
3	chr9:98115200-98125400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:98117400-98118400	Enhancers	HepG2	liver
5	chr9:98117800-98118000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:98117800-98118400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links