Variant report

Variant	rs862476
Chromosome Location	chr14:41993396-41993397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10131184	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10138559	0.90[EUR][1000 genomes]
rs10140527	1.00[CHB][hapmap]
rs10143349	0.94[EUR][1000 genomes]
rs10143445	0.94[EUR][1000 genomes]
rs1103437	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1103438	0.89[EUR][1000 genomes]
rs1111037	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11628212	0.94[EUR][1000 genomes]
rs12437380	0.96[EUR][1000 genomes]
rs12589365	0.85[EUR][1000 genomes]
rs12879030	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12880760	0.90[ASN][1000 genomes]
rs12881237	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17781288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1953700	0.90[EUR][1000 genomes]
rs1953701	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1956445	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1959411	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1959412	0.90[EUR][1000 genomes]
rs1959413	0.90[EUR][1000 genomes]
rs2065968	0.82[ASN][1000 genomes]
rs2415678	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2415682	0.89[EUR][1000 genomes]
rs35583725	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3985189	0.91[EUR][1000 genomes]
rs3985190	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55897228	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58114965	0.85[EUR][1000 genomes]
rs61990270	0.94[EUR][1000 genomes]
rs61990271	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61990273	0.92[EUR][1000 genomes]
rs61990274	0.92[EUR][1000 genomes]
rs61990275	0.92[EUR][1000 genomes]
rs61990277	0.85[EUR][1000 genomes]
rs73309890	0.85[EUR][1000 genomes]
rs862475	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs862478	0.89[EUR][1000 genomes]
rs862479	0.93[EUR][1000 genomes]
rs862480	0.89[EUR][1000 genomes]
rs862481	0.89[EUR][1000 genomes]
rs862482	0.89[EUR][1000 genomes]
rs9806026	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456224	chr14:41432350-42059281	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv564471	chr14:41432350-42059281	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1047300	chr14:41671653-42361098	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1831164	chr14:41673017-42103168	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1044831	chr14:41743218-41997018	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv542057	chr14:41743218-41997018	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1050985	chr14:41770445-42004827	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1043813	chr14:41845956-42005195	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv533968	chr14:41882101-42327882	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3439155	chr14:41984251-42014049	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs862476	LRFN5	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:41991600-41994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:41991600-41994400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr14:41992800-41994200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr14:41993000-41993600	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links