Variant report

Variant	rs4587890
Chromosome Location	chr14:65863784-65863785
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	chr14:65862260..65865116-chr14:65877901..65880398,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000033170	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10138671	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10142283	0.89[CEU][hapmap]
rs10144979	0.89[CEU][hapmap]
rs10152007	0.85[CEU][hapmap]
rs1113962	0.89[CEU][hapmap]
rs11158595	0.85[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs11623662	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11844682	0.85[CEU][hapmap]
rs12433597	0.85[CEU][hapmap]
rs12885842	0.84[CEU][hapmap]
rs1889731	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs1953415	0.85[CEU][hapmap]
rs1953418	0.84[CEU][hapmap]
rs1958559	0.92[CEU][hapmap]
rs1958560	0.92[CEU][hapmap]
rs1959144	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1959145	0.86[ASN][1000 genomes]
rs1999725	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2183277	0.85[CEU][hapmap]
rs2184601	0.89[CEU][hapmap]
rs2210805	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs2411356	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2411815	0.85[CEU][hapmap]
rs2411820	0.89[CEU][hapmap]
rs2411823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898814	0.89[CEU][hapmap]
rs2898818	0.85[CEU][hapmap]
rs3825639	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs4359350	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899178	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902399	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs4902404	0.85[CEU][hapmap]
rs6573609	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6573611	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6573615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6573616	0.85[CEU][hapmap]
rs7140695	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs7141536	0.88[CEU][hapmap]
rs7142906	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7145500	0.83[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.98[ASN][1000 genomes]
rs7145759	0.88[CEU][hapmap]
rs7146993	0.85[CEU][hapmap]
rs7147002	0.85[CEU][hapmap]
rs7147536	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7150448	0.89[CEU][hapmap]
rs7151561	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7157109	0.89[CEU][hapmap]
rs7158153	0.86[CEU][hapmap]
rs7160780	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs8007497	0.85[CEU][hapmap]
rs8010726	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs8011224	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8012834	0.84[ASN][1000 genomes]
rs8013442	0.98[ASN][1000 genomes]
rs8016322	0.83[EUR][1000 genomes]
rs8022053	0.97[ASN][1000 genomes]
rs8022080	0.85[ASN][1000 genomes]
rs9323461	0.85[CEU][hapmap]
rs9972106	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832818	chr14:65706859-65882320	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1044363	chr14:65850832-65870128	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv510639	chr14:65853883-65884315	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4587890	FUT8	cis	cerebellum	SCAN
rs4587890	SIX1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65860200-65874600	Weak transcription	Stomach Mucosa	stomach
2	chr14:65863600-65864600	Enhancers	Primary B cells from peripheral blood	blood

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