Variant report

Variant	rs344028
Chromosome Location	chr3:156465769-156465770
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	chr3:156462787..156465779-chr3:156495644..156498107,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-3	chr3:156465135-156468203	ENSG00000240875
2	lnc-SSR3-3	chr3:156464967-156468203	NONHSAT092863
3	lnc-SSR3-3	chr3:156465132-156468203	NR_038387

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11914959	0.90[JPT][hapmap]
rs11917436	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12497777	0.83[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs13063433	0.87[ASN][1000 genomes]
rs13068223	0.83[TSI][hapmap]
rs1367311	0.83[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs168247	0.96[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs171079	0.82[AFR][1000 genomes]
rs17380702	0.81[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs17380954	0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs184695	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs193197	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2321291	0.90[JPT][hapmap]
rs237250	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343999	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344003	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344018	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs344027	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs344034	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344035	0.84[AMR][1000 genomes]
rs344051	0.82[AFR][1000 genomes]
rs344067	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs345986	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs346003	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	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs386736	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs873337	0.81[JPT][hapmap]
rs8792	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9289971	0.83[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs9871258	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9873307	0.84[ASN][1000 genomes]
rs9882795	0.83[CHB][hapmap];0.90[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
rs344028	Hs.54543	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156446400-156467000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:156447800-156467000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:156460000-156468400	Weak transcription	Pancreas	Pancrea
4	chr3:156462000-156466600	Weak transcription	Right Atrium	heart
5	chr3:156462200-156467000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:156464200-156465800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:156464400-156466400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:156464600-156468000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:156464800-156466800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:156464800-156467200	Weak transcription	Osteobl	bone
11	chr3:156465000-156465800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:156465000-156466400	ZNF genes & repeats	HMEC	breast
13	chr3:156465400-156465800	ZNF genes & repeats	HSMM	muscle
14	chr3:156465400-156466000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:156465400-156467200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:156465600-156466000	Weak transcription	NHEK	skin
17	chr3:156465600-156466200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:156465600-156466200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:156465600-156466400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:156465600-156466600	Weak transcription	A549	lung
21	chr3:156465600-156467200	Weak transcription	NHDF-Ad	bronchial
22	chr3:156465600-156467600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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