Variant report

Variant	rs2939698
Chromosome Location	chr12:45259520-45259521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10506258	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10785535	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10785538	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11524561	0.87[AFR][1000 genomes]
rs11615964	0.85[ASN][1000 genomes]
rs1376126	0.81[ASN][1000 genomes]
rs1506676	0.82[ASN][1000 genomes]
rs1506678	0.82[ASN][1000 genomes]
rs1506679	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506680	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1605296	0.87[AFR][1000 genomes]
rs1605297	0.87[AFR][1000 genomes]
rs1605298	0.87[AFR][1000 genomes]
rs1876241	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2408084	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2408085	0.82[AMR][1000 genomes]
rs2465108	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2465109	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2465110	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2658948	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2658951	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2658954	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2658957	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2658959	0.87[AFR][1000 genomes]
rs2658965	0.87[AFR][1000 genomes]
rs2658966	0.87[AFR][1000 genomes]
rs2710457	0.87[AFR][1000 genomes]
rs2710459	0.87[AFR][1000 genomes]
rs2710461	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2939697	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4238095	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4499065	0.84[AMR][1000 genomes]
rs4768075	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7295923	0.85[ASN][1000 genomes]
rs7304472	0.85[ASN][1000 genomes]
rs7312377	0.89[ASN][1000 genomes]
rs7952764	0.82[ASN][1000 genomes]
rs7979717	0.81[ASN][1000 genomes]
rs884259	0.87[AFR][1000 genomes]
rs884260	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45248600-45259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:45256600-45259800	Weak transcription	Fetal Brain Female	brain
3	chr12:45257000-45266800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:45257400-45259800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:45257400-45259800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:45257400-45265200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:45258200-45259600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:45258200-45260800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:45258600-45259800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:45258600-45265600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:45258600-45267800	Weak transcription	Brain Germinal Matrix	brain
12	chr12:45258800-45259600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:45258800-45259600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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