Variant report

Variant	rs7757317
Chromosome Location	chr6:119753856-119753857
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	chr6:119670600..119672144-chr6:119753052..119754839,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111885	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1112369	0.91[ASN][1000 genomes]
rs11153828	0.89[ASN][1000 genomes]
rs12660903	0.87[ASN][1000 genomes]
rs12661049	0.87[ASN][1000 genomes]
rs12665378	0.88[ASN][1000 genomes]
rs1288080	0.93[ASN][1000 genomes]
rs1288081	0.93[ASN][1000 genomes]
rs1295386	0.82[LWK][hapmap]
rs1318271	0.91[ASN][1000 genomes]
rs1341490	0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs1353864	0.91[ASN][1000 genomes]
rs1392090	0.91[ASN][1000 genomes]
rs1499562	0.86[ASN][1000 genomes]
rs1499566	0.86[ASN][1000 genomes]
rs1499569	0.91[ASN][1000 genomes]
rs1553171	0.89[ASN][1000 genomes]
rs17081283	0.91[ASN][1000 genomes]
rs17081375	0.87[ASN][1000 genomes]
rs17081423	0.94[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1813894	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1875056	0.93[ASN][1000 genomes]
rs1963055	0.91[ASN][1000 genomes]
rs2036256	0.87[ASN][1000 genomes]
rs2066353	0.91[ASN][1000 genomes]
rs2153823	0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs2185752	0.91[ASN][1000 genomes]
rs2185754	0.89[ASN][1000 genomes]
rs2357523	0.86[ASN][1000 genomes]
rs34594936	0.86[ASN][1000 genomes]
rs3778111	0.88[LWK][hapmap]
rs3891962	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4142250	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4142806	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs4551205	0.87[ASN][1000 genomes]
rs4613849	0.87[ASN][1000 genomes]
rs4945637	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4945640	0.91[ASN][1000 genomes]
rs4945642	0.88[ASN][1000 genomes]
rs4945644	0.86[ASN][1000 genomes]
rs4946417	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4946419	0.87[ASN][1000 genomes]
rs4946420	0.91[ASN][1000 genomes]
rs4946423	0.89[ASN][1000 genomes]
rs4946424	0.87[ASN][1000 genomes]
rs4946426	0.87[ASN][1000 genomes]
rs4946427	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs55901595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56081039	0.87[ASN][1000 genomes]
rs56091753	0.89[ASN][1000 genomes]
rs56346325	0.87[ASN][1000 genomes]
rs6913097	0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs6918211	0.91[ASN][1000 genomes]
rs6923080	0.91[ASN][1000 genomes]
rs6935310	0.91[ASN][1000 genomes]
rs6936781	0.86[ASN][1000 genomes]
rs6940248	0.87[ASN][1000 genomes]
rs742962	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7452780	0.87[ASN][1000 genomes]
rs7745025	0.94[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs7768102	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs904574	0.84[ASN][1000 genomes]
rs9320694	0.94[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs9372541	0.86[ASN][1000 genomes]
rs9385073	0.91[ASN][1000 genomes]
rs9387652	0.91[ASN][1000 genomes]
rs9401152	0.86[ASN][1000 genomes]
rs9481911	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9481922	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9481923	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9481924	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9481927	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9481929	0.94[ASN][1000 genomes]
rs9481930	0.93[ASN][1000 genomes]
rs9481931	0.93[ASN][1000 genomes]
rs9481933	0.91[ASN][1000 genomes]
rs9481936	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs9489698	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9489709	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9489710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489714	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9489715	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9489716	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9489717	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9489718	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9489719	0.93[ASN][1000 genomes]
rs9489720	0.91[ASN][1000 genomes]
rs9489723	0.89[ASN][1000 genomes]
rs9489724	0.89[ASN][1000 genomes]
rs9489725	0.87[ASN][1000 genomes]
rs9489727	0.87[ASN][1000 genomes]
rs9489728	0.87[ASN][1000 genomes]
rs9489729	0.87[ASN][1000 genomes]
rs9489731	0.87[ASN][1000 genomes]
rs9489733	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs9885803	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1027904	chr6:119709488-120001986	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv533518	chr6:119712186-119998618	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3442553	chr6:119742069-120076777	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv1845804	chr6:119747112-119771715	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7757317	PLXND1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119748200-119767000	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:119749800-119755000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:119753600-119755000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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