Variant report

Variant	rs1866835
Chromosome Location	chr4:80547253-80547254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10022663	0.89[EUR][1000 genomes]
rs1031005	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs11098770	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs11098788	1.00[ASN][1000 genomes]
rs11098789	0.98[ASN][1000 genomes]
rs11728755	0.85[EUR][1000 genomes]
rs11941782	0.89[EUR][1000 genomes]
rs12643491	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs13104009	0.91[EUR][1000 genomes]
rs13112067	0.89[EUR][1000 genomes]
rs13112577	0.89[EUR][1000 genomes]
rs1371989	0.91[EUR][1000 genomes]
rs1371993	0.90[EUR][1000 genomes]
rs1440853	0.91[EUR][1000 genomes]
rs1837645	0.87[EUR][1000 genomes]
rs1837646	0.87[EUR][1000 genomes]
rs2165386	0.91[EUR][1000 genomes]
rs2582681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2709847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3109166	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3943669	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs4389603	0.91[EUR][1000 genomes]
rs4975056	0.91[EUR][1000 genomes]
rs62297619	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62297620	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62297622	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6812760	0.91[EUR][1000 genomes]
rs6850999	0.91[EUR][1000 genomes]
rs7688923	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs894054	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs894055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9307545	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs9307551	0.90[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
rs1866835	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs1866835	LINC00989	cis	Whole Blood	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80541800-80548600	Enhancers	Rectal Smooth Muscle	rectum
2	chr4:80545000-80551400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:80545000-80555400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:80545400-80555200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:80546600-80547800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:80546600-80547800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:80546800-80547400	Flanking Active TSS	Colon Smooth Muscle	Colon
8	chr4:80546800-80547400	Active TSS	Duodenum Mucosa	Duodenum
9	chr4:80546800-80547600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr4:80546800-80547600	Active TSS	Monocytes-CD14+_RO01746	blood
11	chr4:80546800-80547800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:80547000-80547400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:80547000-80547400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:80547000-80547400	Active TSS	Stomach Smooth Muscle	stomach
15	chr4:80547000-80547600	Enhancers	Primary B cells from peripheral blood	blood
16	chr4:80547000-80547600	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr4:80547000-80547600	Active TSS	Right Atrium	heart
18	chr4:80547000-80547600	Enhancers	NHEK	skin
19	chr4:80547000-80548400	Enhancers	Fetal Brain Male	brain
20	chr4:80547000-80552800	Weak transcription	K562	blood
21	chr4:80547200-80547400	Flanking Active TSS	Osteobl	bone
22	chr4:80547200-80547600	Active TSS	Muscle Satellite Cultured Cells	--
23	chr4:80547200-80547600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:80547200-80547600	Active TSS	Adipose Nuclei	Adipose
25	chr4:80547200-80547600	Active TSS	Fetal Brain Female	brain
26	chr4:80547200-80547600	Active TSS	Hela-S3	cervix
27	chr4:80547200-80547800	Active TSS	Fetal Lung	lung
28	chr4:80547200-80547800	Active TSS	Ovary	ovary
29	chr4:80547200-80548000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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