Variant report

Variant	rs58520085
Chromosome Location	chr2:233578904-233578905
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	chr2:233565184..233567187-chr2:233578536..233582412,3	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11883745	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11883794	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11884898	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11885497	0.95[EUR][1000 genomes]
rs11885646	0.97[EUR][1000 genomes]
rs11890879	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11892639	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11894688	0.85[EUR][1000 genomes]
rs11897789	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11900295	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11900327	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11901015	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11904714	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2271702	0.83[EUR][1000 genomes]
rs2289913	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2289916	0.93[ASN][1000 genomes]
rs2293781	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305138	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2344614	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2880899	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34487721	0.83[EUR][1000 genomes]
rs3738904	0.85[EUR][1000 genomes]
rs3816336	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817310	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4144794	1.00[EUR][1000 genomes]
rs55686138	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55913849	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56140815	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56344253	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56357073	0.81[EUR][1000 genomes]
rs56953250	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57092158	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57211905	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57513852	0.83[EUR][1000 genomes]
rs57657135	0.98[EUR][1000 genomes]
rs57667610	0.83[EUR][1000 genomes]
rs57986228	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58268778	0.85[EUR][1000 genomes]
rs58466616	0.93[EUR][1000 genomes]
rs58835825	0.83[EUR][1000 genomes]
rs59488869	0.85[EUR][1000 genomes]
rs59502980	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59514271	0.98[EUR][1000 genomes]
rs59667905	0.85[EUR][1000 genomes]
rs60103392	0.83[EUR][1000 genomes]
rs60532570	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61518838	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6719766	0.83[EUR][1000 genomes]
rs73092767	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73092790	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102244	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73102257	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73102286	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73106355	0.83[EUR][1000 genomes]
rs73106363	0.85[EUR][1000 genomes]
rs73107693	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73108328	0.83[EUR][1000 genomes]
rs73108346	0.85[EUR][1000 genomes]
rs73999704	0.81[EUR][1000 genomes]
rs73999707	0.85[EUR][1000 genomes]
rs7560000	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7564410	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7578385	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7598518	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7601559	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7606011	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233563800-233582600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:233564000-233579600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:233564000-233589000	Weak transcription	NH-A	brain
4	chr2:233564200-233596400	Weak transcription	NHLF	lung
5	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:233564800-233592800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
8	chr2:233565200-233589800	Weak transcription	HMEC	breast
9	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
10	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
11	chr2:233565400-233580200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:233565400-233589800	Weak transcription	Hela-S3	cervix
13	chr2:233565400-233590000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:233566000-233584600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
17	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr2:233568200-233583800	Strong transcription	HepG2	liver
19	chr2:233568200-233585400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:233568400-233585000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr2:233569000-233582000	Weak transcription	Brain Anterior Caudate	brain
22	chr2:233569000-233585600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:233569200-233579600	Weak transcription	Brain Substantia Nigra	brain
24	chr2:233569200-233589000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:233569200-233590000	Weak transcription	NHDF-Ad	bronchial
26	chr2:233569200-233615000	Weak transcription	Colonic Mucosa	Colon
27	chr2:233569400-233581000	Weak transcription	Pancreas	Pancrea
28	chr2:233569400-233612800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:233569400-233615400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:233570400-233581200	Weak transcription	Psoas Muscle	Psoas
31	chr2:233570600-233593400	Weak transcription	Aorta	Aorta
32	chr2:233570800-233582400	Weak transcription	Spleen	Spleen
33	chr2:233571000-233579400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:233571200-233581200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:233571200-233582400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:233571200-233593600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:233571200-233598200	Weak transcription	Fetal Kidney	kidney
38	chr2:233571200-233627400	Weak transcription	Gastric	stomach
39	chr2:233571400-233581000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:233571400-233582400	Weak transcription	Left Ventricle	heart
41	chr2:233571400-233585600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:233571400-233588600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:233571400-233601800	Weak transcription	Esophagus	oesophagus
44	chr2:233571600-233585600	Weak transcription	Right Ventricle	heart
45	chr2:233571600-233612200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:233572000-233579600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:233572200-233581600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:233572200-233585600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:233572200-233589000	Weak transcription	Osteobl	bone
50	chr2:233572200-233589800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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