Variant report

Variant	rs4859643
Chromosome Location	chr4:77164549-77164550
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:77157429..77161851-chr4:77161856..77166558,5	MCF-7	breast:
2	chr4:77155513..77160129-chr4:77161084..77164552,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189157	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10004443	0.86[ASN][1000 genomes]
rs11097313	0.82[JPT][hapmap]
rs11531413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12643198	0.93[ASN][1000 genomes]
rs12643261	0.82[JPT][hapmap]
rs13114306	0.86[ASN][1000 genomes]
rs13117238	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13122345	0.81[JPT][hapmap]
rs13136819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13137733	0.86[JPT][hapmap]
rs13140675	0.86[ASN][1000 genomes]
rs13150767	0.86[ASN][1000 genomes]
rs1441903	0.86[ASN][1000 genomes]
rs1441910	0.81[JPT][hapmap]
rs1441914	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1441920	0.91[ASN][1000 genomes]
rs1583943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1588214	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1596115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1596116	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1596117	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17236158	0.82[JPT][hapmap]
rs17308336	0.82[JPT][hapmap]
rs1828138	0.86[ASN][1000 genomes]
rs1837867	0.81[ASN][1000 genomes]
rs1876536	0.82[JPT][hapmap]
rs1876539	0.81[JPT][hapmap]
rs1948997	0.81[ASN][1000 genomes]
rs2119731	0.91[CEU][hapmap]
rs2289514	0.92[CEU][hapmap]
rs2869864	0.82[JPT][hapmap]
rs34385906	0.86[ASN][1000 genomes]
rs34846125	0.86[ASN][1000 genomes]
rs35472515	0.86[ASN][1000 genomes]
rs35507310	0.85[ASN][1000 genomes]
rs36031249	0.84[ASN][1000 genomes]
rs36121867	0.86[ASN][1000 genomes]
rs3733250	0.81[JPT][hapmap]
rs4321663	0.86[ASN][1000 genomes]
rs4859430	0.86[ASN][1000 genomes]
rs4859431	0.86[ASN][1000 genomes]
rs4859432	0.86[ASN][1000 genomes]
rs4859434	0.81[ASN][1000 genomes]
rs4859436	0.86[ASN][1000 genomes]
rs4859437	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4859635	0.81[ASN][1000 genomes]
rs4859641	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4859642	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859646	0.91[ASN][1000 genomes]
rs4859648	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs56896076	0.91[ASN][1000 genomes]
rs60225905	0.86[ASN][1000 genomes]
rs6813980	0.92[CEU][hapmap]
rs6817492	0.81[ASN][1000 genomes]
rs6817956	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823078	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6846983	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6849069	0.92[CEU][hapmap]
rs6851219	0.81[JPT][hapmap]
rs71607345	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs717239	0.81[CEU][hapmap]
rs7677256	0.92[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760851	chr4:77164549-77185144	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4859643	FAM47E	cis	cerebellum	SCAN
rs4859643	FAM47E	cis	parietal	SCAN
rs4859643	ANKRD56	cis	parietal	SCAN
rs4859643	SHROOM3	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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