Variant report

Variant	rs2109268
Chromosome Location	chr14:72411855-72411856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72410955..72413262-chr14:72418507..72421384,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1009018	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs1978226	0.88[CEU][hapmap]
rs2190871	0.86[CEU][hapmap]
rs2190872	0.87[CEU][hapmap]
rs2190874	0.93[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs2215133	0.80[EUR][1000 genomes]
rs2238285	0.90[GIH][hapmap]
rs23219	0.91[GIH][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs2332706	0.81[CEU][hapmap]
rs2877772	0.83[EUR][1000 genomes]
rs2877773	0.80[EUR][1000 genomes]
rs36319	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs36320	0.80[EUR][1000 genomes]
rs36322	0.80[EUR][1000 genomes]
rs36323	0.80[EUR][1000 genomes]
rs36324	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs36325	0.80[EUR][1000 genomes]
rs36328	0.80[EUR][1000 genomes]
rs36329	0.83[EUR][1000 genomes]
rs36330	0.80[EUR][1000 genomes]
rs36331	0.93[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs36333	0.80[EUR][1000 genomes]
rs36334	0.80[EUR][1000 genomes]
rs36337	0.80[EUR][1000 genomes]
rs36338	0.83[EUR][1000 genomes]
rs36339	0.80[EUR][1000 genomes]
rs4243639	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs4598834	0.93[CEU][hapmap];0.82[TSI][hapmap]
rs4899406	0.93[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4899408	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs4902959	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs4902962	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs4902967	0.86[CEU][hapmap];0.86[TSI][hapmap]
rs4902968	0.86[CEU][hapmap]
rs4902969	0.93[CEU][hapmap];0.82[TSI][hapmap]
rs4902970	0.86[CEU][hapmap]
rs4902972	0.93[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs61996396	0.80[EUR][1000 genomes]
rs6574036	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7161413	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs722975	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs728494	0.92[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs728495	1.00[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs728498	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs758236	1.00[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs8004427	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs8011972	0.93[CEU][hapmap];0.82[TSI][hapmap]
rs8014500	0.86[CEU][hapmap]
rs917392	0.86[CEU][hapmap]
rs991890	0.93[CEU][hapmap];0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2109268	RGS6	cis	cerebellum	SCAN
rs2109268	TMEM229B	cis	cerebellum	SCAN
rs2109268	HEATR4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72408600-72412600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr14:72409400-72412600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr14:72410600-72412400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:72410600-72425400	Weak transcription	Left Ventricle	heart
5	chr14:72411000-72412800	Weak transcription	GM12878-XiMat	blood
6	chr14:72411600-72412400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr14:72411800-72415600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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