Variant report

Variant	rs10497600
Chromosome Location	chr2:183280294-183280295
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:183279805..183282576-chr2:183283431..183285947,2	MCF-7	breast:
2	chr2:183279201..183281730-chr2:183282038..183284679,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10207132	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10497598	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10497602	0.88[LWK][hapmap]
rs10931012	0.84[JPT][hapmap]
rs11684406	0.84[JPT][hapmap]
rs11686025	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap]
rs13407156	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1367203	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1430147	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1430148	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1430158	0.84[JPT][hapmap]
rs1583114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16823233	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16823254	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16823257	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17265027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17265041	0.80[ASN][1000 genomes]
rs17265061	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17356152	0.85[CEU][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.80[ASN][1000 genomes]
rs17356166	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17356207	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17356214	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1946815	0.85[CEU][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.80[ASN][1000 genomes]
rs28569979	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34103461	1.00[CEU][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62188260	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62188266	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62188267	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62188268	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62188269	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62188270	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62188283	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62188284	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62188286	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62188287	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62188288	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62188289	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62188290	0.87[EUR][1000 genomes]
rs62190201	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	nsv533782	chr2:183059730-183500040	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv834481	chr2:183189758-183339577	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10497600	SSFA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183260800-183281600	Weak transcription	Aorta	Aorta
2	chr2:183272000-183285000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:183277800-183283400	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:183278000-183281800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:183279200-183283400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:183279200-183283400	Weak transcription	Fetal Stomach	stomach
7	chr2:183279800-183281600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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