Variant report

Variant	rs1423358
Chromosome Location	chr5:70750597-70750598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr5:70750546-70752256	SK-N-SH	brain:	n/a	chr5:70751405-70751414

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:70742035..70743794-chr5:70750287..70752992,2	MCF-7	breast:
2	chr5:70749978..70751854-chr5:70881938..70884932,2	K562	blood:

Variant related genes	Relation type
BDP1	TF binding region
ENSG00000250387	Chromatin interaction
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10942466	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10942683	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11740849	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11742923	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11744961	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12109984	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12110291	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12514575	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12520417	0.84[EUR][1000 genomes]
rs12653037	0.80[ASN][1000 genomes]
rs12658383	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13153636	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13158264	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13165848	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13168805	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13175174	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13185743	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs149114	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1559260	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs156753	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs156754	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs156755	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs157044	0.82[EUR][1000 genomes]
rs1698063	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17334377	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs182190	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1833856	0.82[AMR][1000 genomes]
rs1961760	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2059192	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2059193	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2059194	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2059195	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2315519	0.83[ASN][1000 genomes]
rs2315534	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2432059	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2432060	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2454086	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2646639	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2652615	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276590	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs276591	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs276592	0.94[EUR][1000 genomes]
rs276593	0.82[EUR][1000 genomes]
rs276594	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs276595	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs276597	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs276598	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs276600	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs276601	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs277939	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs277940	0.86[EUR][1000 genomes]
rs277948	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs277954	0.80[AMR][1000 genomes]
rs277969	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs277979	0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs277980	0.96[CEU][hapmap];0.84[CHB][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs277996	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs278000	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs279290	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs279291	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs279322	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34029702	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34117302	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35327154	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35420270	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35696325	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36036841	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761965	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3761967	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs384732	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3890749	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs392791	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs410776	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs418738	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4337836	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs439698	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs441691	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4421086	0.86[ASN][1000 genomes]
rs4512120	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs451229	0.80[EUR][1000 genomes]
rs458150	0.85[EUR][1000 genomes]
rs458534	0.81[ASN][1000 genomes]
rs459787	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs460778	0.82[AMR][1000 genomes]
rs464182	0.81[AMR][1000 genomes]
rs467160	0.84[EUR][1000 genomes]
rs467563	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs467620	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs467901	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs468128	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs468467	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs469548	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703986	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4704049	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs541035	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs560394	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56399551	0.80[ASN][1000 genomes]
rs62361813	0.82[EUR][1000 genomes]
rs62374360	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66528760	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6871754	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6881126	0.82[ASN][1000 genomes]
rs6885523	0.81[AMR][1000 genomes]
rs715748	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71624243	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7442961	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7443763	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7444320	0.82[AMR][1000 genomes]
rs7447146	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7447545	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7448221	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7448990	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7702940	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7726336	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7732361	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737101	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9791120	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs986217	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv528571	chr5:70679626-70767269	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv882176	chr5:70738250-70860665	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1423358	FOXD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70746800-70751000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:70747000-70750800	Weak transcription	Pancreas	Pancrea
3	chr5:70748600-70750800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:70750400-70751000	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links