Variant report

Variant	rs29509
Chromosome Location	chr7:41204199-41204200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:41203420..41205145-chr7:41207158..41208668,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10242681	0.89[CEU][hapmap]
rs12670349	0.92[CEU][hapmap]
rs12701875	0.89[CEU][hapmap]
rs13222193	0.92[CEU][hapmap]
rs13222281	0.92[CEU][hapmap]
rs13234888	0.92[CEU][hapmap]
rs1859692	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1859694	0.86[EUR][1000 genomes]
rs2108155	0.81[EUR][1000 genomes]
rs2190329	0.91[EUR][1000 genomes]
rs28176	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28238	0.91[ASN][1000 genomes]
rs28314	0.90[ASN][1000 genomes]
rs29479	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29480	0.92[EUR][1000 genomes]
rs29481	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29483	0.90[ASN][1000 genomes]
rs29484	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs29485	0.90[ASN][1000 genomes]
rs29486	0.90[ASN][1000 genomes]
rs29488	0.90[ASN][1000 genomes]
rs29489	0.90[ASN][1000 genomes]
rs29490	0.90[ASN][1000 genomes]
rs29492	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29493	0.91[ASN][1000 genomes]
rs29494	0.88[ASN][1000 genomes]
rs29495	0.91[ASN][1000 genomes]
rs29496	0.91[ASN][1000 genomes]
rs29497	0.91[ASN][1000 genomes]
rs29498	0.91[ASN][1000 genomes]
rs29499	0.90[ASN][1000 genomes]
rs29500	0.91[ASN][1000 genomes]
rs29501	0.91[ASN][1000 genomes]
rs29502	0.91[ASN][1000 genomes]
rs29503	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs29504	0.91[ASN][1000 genomes]
rs29505	0.91[ASN][1000 genomes]
rs29506	0.91[ASN][1000 genomes]
rs29508	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29511	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29512	0.87[ASN][1000 genomes]
rs29513	0.87[ASN][1000 genomes]
rs29514	0.87[ASN][1000 genomes]
rs29515	0.87[ASN][1000 genomes]
rs29516	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs29517	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29518	0.87[ASN][1000 genomes]
rs29519	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs29521	0.87[ASN][1000 genomes]
rs29522	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs29523	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs29524	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs29525	0.87[ASN][1000 genomes]
rs29526	0.87[ASN][1000 genomes]
rs6945256	0.85[EUR][1000 genomes]
rs6947021	0.87[EUR][1000 genomes]
rs6951425	1.00[CHB][hapmap]
rs6958959	0.87[EUR][1000 genomes]
rs6970635	0.80[EUR][1000 genomes]
rs6975061	0.84[EUR][1000 genomes]
rs6978132	0.88[EUR][1000 genomes]
rs7384944	0.85[ASN][1000 genomes]
rs7796964	0.89[CEU][hapmap]
rs7799191	0.80[EUR][1000 genomes]
rs9632615	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034605	chr7:41096638-41222426	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv887989	chr7:41125447-41337044	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1028983	chr7:41165668-41635954	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs29509	MYL7	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:41189400-41222400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:41202000-41204200	Enhancers	NHDF-Ad	bronchial
3	chr7:41203400-41204200	Enhancers	HSMMtube	muscle
4	chr7:41203400-41204400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr7:41203400-41204600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:41203600-41204400	Enhancers	HSMM	muscle
7	chr7:41203600-41204600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:41203800-41204400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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