Variant report

Variant	rs10206939
Chromosome Location	chr2:54564091-54564092
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	chr2:54555822..54558489-chr2:54561441..54564836,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177994	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10168899	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10177706	1.00[AMR][1000 genomes]
rs10182439	1.00[AMR][1000 genomes]
rs10184091	1.00[AMR][1000 genomes]
rs10184388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10190817	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10192536	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10192849	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10193885	1.00[AMR][1000 genomes]
rs10195165	1.00[AMR][1000 genomes]
rs10195657	1.00[AMR][1000 genomes]
rs10196054	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10206181	1.00[AMR][1000 genomes]
rs10207434	1.00[AMR][1000 genomes]
rs10207830	1.00[AMR][1000 genomes]
rs10209379	1.00[AMR][1000 genomes]
rs10210249	1.00[AMR][1000 genomes]
rs11125530	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13383434	1.00[AMR][1000 genomes]
rs13386127	1.00[AMR][1000 genomes]
rs13386211	1.00[AMR][1000 genomes]
rs13389240	1.00[AMR][1000 genomes]
rs13390991	1.00[AMR][1000 genomes]
rs13392879	1.00[AMR][1000 genomes]
rs13392982	1.00[AMR][1000 genomes]
rs13393792	1.00[AMR][1000 genomes]
rs13396310	1.00[AMR][1000 genomes]
rs13396318	1.00[AMR][1000 genomes]
rs13403112	1.00[AMR][1000 genomes]
rs13404835	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13407955	1.00[AMR][1000 genomes]
rs13410757	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13411424	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13411458	1.00[AMR][1000 genomes]
rs13415033	1.00[AMR][1000 genomes]
rs13415558	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13419158	1.00[AMR][1000 genomes]
rs13423383	1.00[AMR][1000 genomes]
rs13423617	1.00[AMR][1000 genomes]
rs13423698	1.00[AMR][1000 genomes]
rs13425423	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13431239	1.00[AMR][1000 genomes]
rs28607569	1.00[AMR][1000 genomes]
rs28698214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9808395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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
19	nsv436294	chr2:54562596-54568259	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	esv3456943	chr2:54563548-54569446	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54558800-54574800	Weak transcription	Left Ventricle	heart
2	chr2:54559000-54568400	Weak transcription	Right Ventricle	heart
3	chr2:54562000-54564800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:54562000-54565400	Enhancers	Fetal Heart	heart
5	chr2:54562200-54565000	Enhancers	HSMM	muscle
6	chr2:54562400-54565000	Enhancers	NHDF-Ad	bronchial
7	chr2:54562600-54564600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:54562600-54565400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:54562800-54564400	Enhancers	NH-A	brain
10	chr2:54562800-54565200	Enhancers	Osteobl	bone
11	chr2:54562800-54565400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:54563000-54564800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:54563200-54564600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:54563200-54568600	Weak transcription	Right Atrium	heart
15	chr2:54563400-54564200	Enhancers	Aorta	Aorta
16	chr2:54563400-54564200	Enhancers	Colon Smooth Muscle	Colon
17	chr2:54563400-54564400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:54563400-54564400	Enhancers	Brain Cingulate Gyrus	brain
19	chr2:54563400-54564400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr2:54563400-54564400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr2:54563600-54564200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:54563600-54564400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:54563600-54564600	Enhancers	Brain Anterior Caudate	brain
24	chr2:54563800-54564200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:54563800-54564200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:54563800-54564200	Enhancers	Adipose Nuclei	Adipose
27	chr2:54563800-54564200	Enhancers	Brain Substantia Nigra	brain
28	chr2:54563800-54564200	Enhancers	Fetal Brain Female	brain
29	chr2:54563800-54564200	Enhancers	Lung	lung
30	chr2:54563800-54564400	Enhancers	Brain Angular Gyrus	brain
31	chr2:54563800-54564600	Enhancers	Brain Hippocampus Middle	brain
32	chr2:54563800-54564600	Flanking Active TSS	NHLF	lung
33	chr2:54564000-54564200	Enhancers	HSMMtube	muscle

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