Variant report

Variant	rs6978281
Chromosome Location	chr7:80884841-80884842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:80884647..80887229-chr7:80899126..80901449,2	MCF-7	breast:
2	chr7:80874756..80878864-chr7:80882916..80885687,3	MCF-7	breast:
3	chr7:80545834..80553200-chr7:80879354..80888784,34	MCF-7	breast:
4	chr7:80878967..80881454-chr7:80884468..80886098,2	MCF-7	breast:
5	chr7:80883750..80886703-chr7:80894705..80896223,2	MCF-7	breast:
6	chr7:80788690..80790506-chr7:80884567..80886518,2	MCF-7	breast:
7	chr7:80538890..80541410-chr7:80883326..80886321,2	MCF-7	breast:
8	chr7:80568637..80573447-chr7:80883895..80888715,7	MCF-7	breast:
9	chr7:80569987..80572851-chr7:80884552..80889761,8	MCF-7	breast:
10	chr7:80884770..80887178-chr7:81075259..81077204,2	MCF-7	breast:
11	chr7:80544766..80552951-chr7:80883361..80891908,25	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000075223	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10226419	1.00[ASN][1000 genomes]
rs10233336	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10239348	1.00[ASN][1000 genomes]
rs10240850	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10240984	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10251275	1.00[ASN][1000 genomes]
rs10253284	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10256727	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10256970	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10261434	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]
rs10264197	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];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10269971	1.00[ASN][1000 genomes]
rs10271152	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10271782	1.00[ASN][1000 genomes]
rs10275968	0.88[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10277220	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10279555	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10280072	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11971159	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11971296	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11972566	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11983851	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13347373	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1397013	1.00[MEX][hapmap]
rs1533070	1.00[MEX][hapmap]
rs28544451	1.00[ASN][1000 genomes]
rs28748026	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs327696	1.00[MEX][hapmap]
rs55781761	1.00[ASN][1000 genomes]
rs61259831	1.00[ASN][1000 genomes]
rs73382462	1.00[ASN][1000 genomes]
rs73382467	1.00[ASN][1000 genomes]
rs7787168	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7789539	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7789729	0.84[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7791322	1.00[ASN][1000 genomes]
rs7791375	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7799259	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7811171	1.00[ASN][1000 genomes]
rs9656473	1.00[ASN][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
rs6978281	PYDC2	trans	lymphoblastoid	seeQTL

Chromatin state (count:1 , 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

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