Variant report

Variant	rs2582681
Chromosome Location	chr4:80544218-80544219
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	chr17:59884431..59885001-chr4:80544092..80544675,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10022663	0.91[EUR][1000 genomes]
rs1031005	0.92[EUR][1000 genomes]
rs11098770	0.93[EUR][1000 genomes]
rs11098788	0.97[ASN][1000 genomes]
rs11098789	0.95[ASN][1000 genomes]
rs11728755	0.87[EUR][1000 genomes]
rs11941782	0.91[EUR][1000 genomes]
rs12643491	0.93[EUR][1000 genomes]
rs13104009	0.93[EUR][1000 genomes]
rs13112067	0.91[EUR][1000 genomes]
rs13112577	0.91[EUR][1000 genomes]
rs1371989	0.93[EUR][1000 genomes]
rs1371993	0.92[EUR][1000 genomes]
rs1440853	0.93[EUR][1000 genomes]
rs1837645	0.89[EUR][1000 genomes]
rs1837646	0.90[EUR][1000 genomes]
rs1866835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2165386	0.93[EUR][1000 genomes]
rs2709847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109166	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3943669	0.93[EUR][1000 genomes]
rs4389603	0.93[EUR][1000 genomes]
rs4975056	0.93[EUR][1000 genomes]
rs62297619	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62297620	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62297622	0.86[AMR][1000 genomes]
rs6812760	0.93[EUR][1000 genomes]
rs6850999	0.93[EUR][1000 genomes]
rs7688923	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs894054	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs894055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307545	0.93[EUR][1000 genomes]
rs9307551	0.92[EUR][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	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv879507	chr4:80365765-80552199	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv879508	chr4:80398708-80552199	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2582681	LINC00989	cis	Whole Blood	GTEx
rs2582681	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80541800-80548600	Enhancers	Rectal Smooth Muscle	rectum
2	chr4:80543200-80546600	Weak transcription	K562	blood
3	chr4:80543600-80544600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:80543600-80544600	Enhancers	Colon Smooth Muscle	Colon
5	chr4:80543600-80544600	Enhancers	Fetal Lung	lung
6	chr4:80543600-80545400	Enhancers	Fetal Stomach	stomach
7	chr4:80543800-80544400	Enhancers	Osteobl	bone
8	chr4:80543800-80544600	Enhancers	Brain Germinal Matrix	brain
9	chr4:80543800-80544600	Flanking Active TSS	Fetal Brain Male	brain
10	chr4:80544000-80544400	Active TSS	Fetal Brain Female	brain
11	chr4:80544000-80544400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr4:80544000-80545000	Active TSS	Aorta	Aorta
13	chr4:80544000-80545000	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr4:80544200-80544400	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr4:80544200-80544400	Enhancers	Right Atrium	heart
16	chr4:80544200-80544400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr4:80544200-80544600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr4:80544200-80544600	Enhancers	Colonic Mucosa	Colon
19	chr4:80544200-80544600	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr4:80544200-80544600	Enhancers	NHDF-Ad	bronchial
21	chr4:80544200-80545000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:80544200-80545000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:80544200-80545200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr4:80544200-80545400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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