Variant report

Variant	rs12892100
Chromosome Location	chr14:72478034-72478035
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	chr14:72471348..72475296-chr14:72476061..72479631,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11623376	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11844049	0.86[AFR][1000 genomes]
rs11850350	0.83[AFR][1000 genomes]
rs11852205	0.86[AFR][1000 genomes]
rs12586947	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12586968	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12883063	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12884202	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12884483	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12885938	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12897386	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2190867	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2215132	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2238268	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2238269	0.85[ASN][1000 genomes]
rs2238270	0.86[ASN][1000 genomes]
rs2239267	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2239268	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2332707	0.88[ASN][1000 genomes]
rs35727014	0.88[ASN][1000 genomes]
rs4048388	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6574037	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs6574038	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8008678	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs8017221	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs8017799	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs966815	0.96[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12892100	FAM71D	cis	parietal	SCAN
rs12892100	ACYP1	cis	cerebellum	SCAN
rs12892100	MPP5	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72475800-72479200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr14:72476000-72480200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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