Variant report

Variant	rs58446150
Chromosome Location	chr6:25014430-25014431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25013763..25015712-chr6:25017838..25021035,3	K562	blood:
2	chr6:25008899..25010659-chr6:25012678..25014567,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GMNN-5	chr6:25013543-25016188	NONHSAT108129

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11964330	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12110508	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12111569	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56772860	0.82[EUR][1000 genomes]
rs58272875	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58858607	0.82[EUR][1000 genomes]
rs59935869	0.82[EUR][1000 genomes]
rs60753079	0.82[EUR][1000 genomes]
rs73384104	0.82[EUR][1000 genomes]
rs73384131	0.82[EUR][1000 genomes]
rs73384137	0.82[EUR][1000 genomes]
rs73384148	0.82[EUR][1000 genomes]
rs73384155	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384157	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384158	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384159	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384162	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384165	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73384168	1.00[EUR][1000 genomes]
rs73384170	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24997800-25016600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:25007400-25014800	Weak transcription	Fetal Brain Male	brain
3	chr6:25007400-25017600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:25007600-25015000	Weak transcription	HSMMtube	muscle
5	chr6:25008000-25014600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:25008000-25014800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:25008000-25014800	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:25008000-25015400	Weak transcription	Right Atrium	heart
9	chr6:25008000-25016600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr6:25008200-25015400	Weak transcription	Gastric	stomach
11	chr6:25009400-25015400	Weak transcription	Esophagus	oesophagus
12	chr6:25010000-25016000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:25010000-25017400	Enhancers	Hela-S3	cervix
14	chr6:25010000-25018000	Enhancers	HMEC	breast
15	chr6:25010400-25014800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:25010400-25015200	Enhancers	NHDF-Ad	bronchial
17	chr6:25010400-25015800	Enhancers	NHLF	lung
18	chr6:25010400-25017200	Enhancers	Osteobl	bone
19	chr6:25010600-25015400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:25010600-25015400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:25010600-25015400	Weak transcription	Lung	lung
22	chr6:25010600-25015400	Weak transcription	Pancreas	Pancrea
23	chr6:25011000-25016800	Enhancers	HSMM	muscle
24	chr6:25011200-25014600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:25011200-25015000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:25011200-25015000	Weak transcription	Fetal Thymus	thymus
27	chr6:25011200-25023400	Weak transcription	Thymus	Thymus
28	chr6:25011200-25035600	Weak transcription	Spleen	Spleen
29	chr6:25011800-25014600	Weak transcription	Primary T cells from cord blood	blood
30	chr6:25011800-25015200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:25012200-25018400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:25012400-25014800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:25012600-25015200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:25012600-25016800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:25012600-25018400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr6:25012600-25018600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr6:25012800-25015200	Weak transcription	Dnd41	blood
38	chr6:25012800-25018600	Enhancers	Primary B cells from peripheral blood	blood
39	chr6:25013000-25016600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr6:25013000-25018200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr6:25013200-25017400	Weak transcription	Placenta	Placenta
42	chr6:25013400-25014600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr6:25013400-25014800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:25013400-25014800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:25013400-25014800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:25013400-25014800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:25013400-25015200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr6:25013400-25015400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:25013400-25016400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:25013600-25015800	Enhancers	GM12878-XiMat	blood

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