Variant report

Variant	rs13000039
Chromosome Location	chr2:54562343-54562344
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	chr2:54560405..54562674-chr2:54570057..54572627,2	MCF-7	breast:
2	chr2:54555822..54558489-chr2:54561441..54564836,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177994	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11895729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904342	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13009959	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13023335	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13184	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34474573	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34567788	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35123043	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35421399	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077591	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57798791	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62138163	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6711656	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6715177	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6739530	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6761635	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs985773	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1004632	chr2:54469283-54590480	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1815958	chr2:54559793-54567092	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv582013	chr2:54559793-54567329	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv582014	chr2:54559793-54567441	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv1823588	chr2:54562012-54567092	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1825251	chr2:54562012-54567092	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1826095	chr2:54562012-54567092	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1830130	chr2:54562012-54567092	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv1849337	chr2:54562069-54567347	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv1837933	chr2:54562069-54567441	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv511174	chr2:54562069-54567590	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13000039	C2orf73	cis	brain	BrainEAC
rs13000039	C2orf73	cis	hippocampus	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54558600-54562600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:54558600-54562800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:54558600-54563000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:54558600-54563400	Weak transcription	Aorta	Aorta
5	chr2:54558600-54563400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:54558800-54562600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:54558800-54562800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:54558800-54562800	Weak transcription	Right Atrium	heart
9	chr2:54558800-54562800	Weak transcription	Osteobl	bone
10	chr2:54558800-54563000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:54558800-54563200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:54558800-54563200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:54558800-54563400	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:54558800-54563800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:54558800-54563800	Weak transcription	Adipose Nuclei	Adipose
16	chr2:54558800-54563800	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:54558800-54563800	Weak transcription	Lung	lung
18	chr2:54558800-54574800	Weak transcription	Left Ventricle	heart
19	chr2:54559000-54563400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:54559000-54563400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:54559000-54563400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:54559000-54568400	Weak transcription	Right Ventricle	heart
23	chr2:54559200-54563600	Weak transcription	Brain Anterior Caudate	brain
24	chr2:54559400-54562400	Weak transcription	NHDF-Ad	bronchial
25	chr2:54559800-54562600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:54562000-54564800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:54562000-54565400	Enhancers	Fetal Heart	heart
28	chr2:54562200-54563800	Enhancers	HSMMtube	muscle
29	chr2:54562200-54563800	Enhancers	NHLF	lung
30	chr2:54562200-54565000	Enhancers	HSMM	muscle

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