Variant report

No.	Distal block	Cell Line	Cell type
1	chr2:64526776..64529071-chr2:64543471..64545003,2	MCF-7	breast:
2	chr2:64542272..64545159-chr2:64546198..64548765,2	MCF-7	breast:
3	chr2:64276818..64280771-chr2:64542300..64544663,3	MCF-7	breast:

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10164841	1.00[JPT][hapmap]
rs10206155	1.00[JPT][hapmap]
rs1030408	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1426704	0.82[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1534684	0.87[EUR][1000 genomes]
rs2555417	0.87[EUR][1000 genomes]
rs2555424	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555429	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2555431	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2555432	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2555447	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555450	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555451	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555454	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698540	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4459720	1.00[JPT][hapmap]
rs6546066	0.86[ASN][1000 genomes]
rs7559505	1.00[JPT][hapmap]
rs7560580	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562531	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930019	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs883021	PELI1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64539800-64549600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:64540000-64554200	Weak transcription	Fetal Brain Female	brain
3	chr2:64540200-64554600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:64540800-64549600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:64540800-64554600	Weak transcription	Right Atrium	heart
6	chr2:64541600-64545600	Weak transcription	Fetal Kidney	kidney
7	chr2:64542200-64547200	Weak transcription	Brain Germinal Matrix	brain
8	chr2:64542800-64545200	Weak transcription	Fetal Lung	lung
9	chr2:64543400-64546000	Enhancers	Fetal Thymus	thymus
10	chr2:64543800-64549000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:64543800-64549400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:64544000-64546000	Enhancers	Thymus	Thymus
13	chr2:64544000-64547800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:64544200-64544600	Enhancers	Pancreas	Pancrea
15	chr2:64544400-64548400	Weak transcription	Fetal Muscle Trunk	muscle

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