Variant report

Variant	rs12080986
Chromosome Location	chr1:86621160-86621161
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ODF2L-3	chr1:86619756-86621905	NONHSAT004264

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11161752	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs11161754	0.80[ASN][1000 genomes]
rs11161755	0.88[CHB][hapmap];0.84[CHD][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs11161756	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs11161757	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs11161758	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs11161759	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs12070992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072489	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs12072806	0.80[ASN][1000 genomes]
rs12074275	0.80[ASN][1000 genomes]
rs12076366	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs1507276	0.88[CHB][hapmap];0.80[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs1507282	0.88[CHB][hapmap];0.81[CHD][hapmap];0.84[MEX][hapmap]
rs1507283	0.86[CHB][hapmap]
rs2892908	0.88[CHB][hapmap];0.84[CHD][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs6660694	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs72716202	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1009092	chr1:86532988-86724805	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535024	chr1:86532988-86724805	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv830481	chr1:86550274-86737290	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2763578	chr1:86584695-86622285	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86617800-86621600	Weak transcription	HSMM	muscle
2	chr1:86619800-86622400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:86620000-86623000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:86620200-86621200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:86620200-86621600	Bivalent Enhancer	Fetal Brain Male	brain
6	chr1:86620200-86622600	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr1:86620200-86623000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:86620200-86623000	Active TSS	Right Atrium	heart
9	chr1:86620400-86621200	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:86620400-86621200	Flanking Active TSS	Colon Smooth Muscle	Colon
11	chr1:86620400-86621200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr1:86620400-86621200	Flanking Bivalent TSS/Enh	NHEK	skin
13	chr1:86620400-86621400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:86620400-86621400	Bivalent Enhancer	HMEC	breast
15	chr1:86620400-86621800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
16	chr1:86620400-86621800	Bivalent Enhancer	Liver	Liver
17	chr1:86620400-86622000	Enhancers	Gastric	stomach
18	chr1:86620400-86622000	Enhancers	Spleen	Spleen
19	chr1:86620400-86622200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr1:86620400-86622200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:86620400-86622600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:86620400-86622600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
23	chr1:86620400-86622600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
24	chr1:86620400-86622800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:86620400-86622800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:86620400-86623000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr1:86620400-86623000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
28	chr1:86620600-86621200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
29	chr1:86620600-86621200	Bivalent Enhancer	Fetal Thymus	thymus
30	chr1:86620600-86621200	Bivalent Enhancer	Left Ventricle	heart
31	chr1:86620600-86621200	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
32	chr1:86620600-86621200	Flanking Active TSS	NHDF-Ad	bronchial
33	chr1:86620600-86621400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:86620600-86621600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
35	chr1:86620600-86621600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
36	chr1:86620600-86621600	Bivalent Enhancer	Placenta	Placenta
37	chr1:86620600-86621600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr1:86620600-86621800	Enhancers	Fetal Heart	heart
39	chr1:86620600-86621800	Bivalent Enhancer	Lung	lung
40	chr1:86620600-86622400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
41	chr1:86620600-86622800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
42	chr1:86620600-86623000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr1:86620600-86623000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr1:86620800-86621200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:86620800-86621200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:86620800-86621400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:86620800-86621600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:86620800-86621600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:86620800-86621800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:86620800-86621800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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