Variant report

Variant	rs344003
Chromosome Location	chr3:156457720-156457721
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	chr3:156455142..156458106-chr3:156458193..156461275,4	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11914959	0.91[JPT][hapmap]
rs11917436	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12497777	0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs13063433	0.87[ASN][1000 genomes]
rs1367311	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs168247	0.92[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17380702	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs17380954	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs184695	1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs193197	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2321291	0.90[JPT][hapmap]
rs237250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343999	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344018	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs344027	0.92[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs344028	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344034	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344035	0.82[AMR][1000 genomes]
rs344067	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs345986	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs346003	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34901284	0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs35161260	0.90[ASN][1000 genomes]
rs374341	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs386736	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs873337	0.81[JPT][hapmap]
rs8792	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9289971	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9871258	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9873307	0.84[ASN][1000 genomes]
rs9882795	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9883439	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs344003	Hs.54543	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156445600-156459600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:156446400-156464600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:156446400-156467000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:156447800-156464200	Weak transcription	HSMM	muscle
5	chr3:156447800-156464600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:156447800-156465000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:156447800-156467000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:156448200-156462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:156448200-156464200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:156448400-156464600	Weak transcription	NHEK	skin
11	chr3:156450400-156459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:156450800-156458600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:156450800-156461600	Weak transcription	HepG2	liver
14	chr3:156456000-156461800	Weak transcription	Fetal Intestine Small	intestine
15	chr3:156457000-156459400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:156457400-156457800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:156457600-156457800	Enhancers	Fetal Muscle Leg	muscle
18	chr3:156457600-156460000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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