Variant report

Variant	rs17279030
Chromosome Location	chr2:56185872-56185873
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:56001464..56004424-chr2:56185372..56187665,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFEMP1-1	chr2:56183727-56185924	NONHSAT070812

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10496056	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs17278953	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867970	1.00[ASN][1000 genomes]
rs34708847	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45535043	1.00[ASN][1000 genomes]
rs6735143	1.00[ASN][1000 genomes]
rs72924567	1.00[ASN][1000 genomes]
rs73940343	1.00[ASN][1000 genomes]
rs9753376	1.00[ASN][1000 genomes]
rs9753385	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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv874161	chr2:56154316-56203798	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
4	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17279030	STS	trans	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56180000-56188800	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:56183800-56186400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:56183800-56186600	Enhancers	Placenta Amnion	Placenta Amnion
4	chr2:56184000-56186000	Weak transcription	Ovary	ovary
5	chr2:56184000-56186400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:56184200-56186600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:56184400-56186600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:56184400-56186600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:56184800-56186400	Enhancers	Placenta	Placenta
10	chr2:56184800-56186800	Enhancers	HMEC	breast
11	chr2:56185000-56186200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr2:56185000-56187000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:56185200-56186000	Enhancers	Stomach Mucosa	stomach
14	chr2:56185200-56186000	Flanking Active TSS	A549	lung
15	chr2:56185200-56186000	Flanking Active TSS	HSMM	muscle
16	chr2:56185200-56186000	Flanking Active TSS	NHEK	skin
17	chr2:56185200-56186200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:56185200-56186400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:56185200-56186400	Enhancers	NH-A	brain
20	chr2:56185200-56186600	Enhancers	HSMMtube	muscle
21	chr2:56185400-56186000	Enhancers	Fetal Lung	lung
22	chr2:56185400-56186000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr2:56185400-56186000	Enhancers	NHLF	lung
24	chr2:56185400-56186200	Enhancers	Colonic Mucosa	Colon
25	chr2:56185600-56186200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:56185800-56186000	Bivalent Enhancer	NHDF-Ad	bronchial
27	chr2:56185800-56186600	Enhancers	Osteobl	bone
28	chr2:56185800-56186800	Enhancers	Hela-S3	cervix
29	chr2:56185800-56187400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:56185800-56188400	Weak transcription	Adipose Nuclei	Adipose

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