Variant report

Variant	rs2238207
Chromosome Location	chr14:72757384-72757385
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	chr14:72749616..72751897-chr14:72756117..72758691,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10146126	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10483843	0.86[MEX][hapmap]
rs12184980	0.86[MEX][hapmap]
rs1996661	0.85[MEX][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes]
rs2079500	0.86[MEX][hapmap]
rs2090736	0.85[AMR][1000 genomes]
rs2108468	0.81[LWK][hapmap]
rs2139596	0.80[TSI][hapmap]
rs2222311	0.96[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs2238195	0.80[MEX][hapmap];0.82[YRI][hapmap]
rs2238204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238205	0.83[AMR][1000 genomes]
rs2238206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239246	0.88[YRI][hapmap]
rs2529476	0.83[AMR][1000 genomes]
rs4899430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6574065	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7151952	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];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152907	0.86[MEX][hapmap]
rs7156910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737498	0.86[MEX][hapmap]
rs737499	0.86[MEX][hapmap]
rs765221	0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs847331	0.90[TSI][hapmap]
rs847334	0.80[TSI][hapmap]
rs847346	0.85[CHD][hapmap]
rs847348	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs847349	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs847350	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs847360	0.88[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap]
rs847362	0.88[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs847364	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[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	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
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1041492	chr14:72634606-72768970	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2238207	TTC9	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72756400-72757800	Enhancers	Fetal Brain Female	brain
2	chr14:72756600-72759200	Enhancers	Fetal Brain Male	brain
3	chr14:72756800-72759600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr14:72757000-72758200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr14:72757200-72758800	Weak transcription	Left Ventricle	heart

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