Variant report

Variant	rs58409854
Chromosome Location	chr12:45748694-45748695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:45608086..45610332-chr12:45748571..45750861,2	K562	blood:
2	chr12:45734366..45736886-chr12:45747224..45749604,2	K562	blood:
3	chr12:45717384..45719924-chr12:45748264..45750670,2	MCF-7	breast:
4	chr12:45617264..45618883-chr12:45748114..45750683,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134297	Chromatin interaction
ENSG00000177119	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12580320	1.00[AFR][1000 genomes]
rs12580810	1.00[AFR][1000 genomes]
rs1316777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1316778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2081592	0.98[AFR][1000 genomes]
rs2162321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3847983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3847984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4108249	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4108250	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55708540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55812173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56408748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57858655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58221634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58824383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59436840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59728495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59789543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60011223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60287166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60457106	1.00[AFR][1000 genomes]
rs60831882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61265799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61349051	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7134442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7294399	1.00[AFR][1000 genomes]
rs7299229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7305478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080884	1.00[AFR][1000 genomes]
rs7956153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7960365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7969594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7969966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7970586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7971106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7974971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7975088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45723800-45757000	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:45725800-45782000	Weak transcription	Brain Angular Gyrus	brain
3	chr12:45735400-45755200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:45737400-45748800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:45738800-45754600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:45739000-45756000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr12:45739200-45752000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:45740400-45755000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:45740800-45757600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:45741000-45752000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:45741400-45755400	Weak transcription	Brain Anterior Caudate	brain
12	chr12:45742600-45750600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:45742800-45758000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:45744200-45750800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:45744200-45751000	Weak transcription	Right Atrium	heart
16	chr12:45744800-45749400	Weak transcription	K562	blood
17	chr12:45744800-45750200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:45744800-45758800	Weak transcription	Psoas Muscle	Psoas
19	chr12:45744800-45809200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:45745000-45749200	Weak transcription	Aorta	Aorta
21	chr12:45745000-45751000	Weak transcription	Fetal Heart	heart
22	chr12:45745000-45751200	Weak transcription	NHDF-Ad	bronchial
23	chr12:45745000-45751800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:45745000-45753800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:45745000-45754000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:45745000-45756800	Weak transcription	Esophagus	oesophagus
27	chr12:45745000-45757000	Weak transcription	Spleen	Spleen
28	chr12:45745000-45762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:45745000-45763600	Weak transcription	Pancreas	Pancrea
30	chr12:45745000-45763800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr12:45745000-45779800	Weak transcription	Gastric	stomach
32	chr12:45745200-45748800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:45745200-45749000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:45745200-45749000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:45745200-45749400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:45745200-45751000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:45745200-45751200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:45745200-45751200	Weak transcription	Osteobl	bone
39	chr12:45745200-45751800	Weak transcription	Fetal Brain Female	brain
40	chr12:45745200-45751800	Weak transcription	NHLF	lung
41	chr12:45745200-45755200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr12:45745200-45755800	Weak transcription	HSMM	muscle
43	chr12:45745200-45756600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:45745400-45749200	Weak transcription	Placenta	Placenta
45	chr12:45745400-45750600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:45745400-45750800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:45745400-45751000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:45745400-45754200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:45745400-45755800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:45745400-45773000	Weak transcription	Hela-S3	cervix

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