Variant report

Variant	rs10261434
Chromosome Location	chr7:80893211-80893212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:80545653..80550046-chr7:80890283..80894244,7	MCF-7	breast:
2	chr7:80570593..80572425-chr7:80891070..80893761,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075223	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10233336	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10240850	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10240984	1.00[AFR][1000 genomes]
rs10253284	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10256727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10256970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10264197	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10271152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10275968	0.86[ASW][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10277220	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10279555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10280072	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11971159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11971296	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11972566	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11983851	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13347373	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1397013	1.00[MEX][hapmap]
rs1533070	1.00[MEX][hapmap]
rs28748026	1.00[AFR][1000 genomes]
rs327696	1.00[MEX][hapmap]
rs6978281	0.84[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7787168	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7789539	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7789729	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7791375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7799259	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034690	chr7:80520004-80987682	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv831044	chr7:80721773-80918591	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv888557	chr7:80813081-80917148	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1023149	chr7:80817550-80928090	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1029034	chr7:80838012-81137146	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv831045	chr7:80841693-81012404	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv888558	chr7:80844667-80917148	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv607686	chr7:80857196-80917148	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv464608	chr7:80866153-80938045	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv607687	chr7:80866153-80938045	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv888559	chr7:80870379-80917148	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv607688	chr7:80870379-80947517	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10261434	PYDC2	trans	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80870800-80893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:80886600-80903000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:80893200-80894000	Enhancers	HMEC	breast

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