Variant report

Variant	rs416030
Chromosome Location	chr6:25071081-25071082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24855908..24856523-chr6:25070777..25071542,2	MCF-7	breast:
2	chr6:24933782..24934728-chr6:25070736..25071642,2	K562	blood:
3	chr6:24855912..24856897-chr6:25070777..25071655,5	K562	blood:
4	chr6:24856035..24856908-chr6:25071041..25071669,3	MCF-7	breast:
5	chr6:24719082..24721541-chr6:25070206..25072923,2	K562	blood:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1665820	0.86[ASN][1000 genomes]
rs182499	1.00[ASN][1000 genomes]
rs188567	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28539031	0.86[ASN][1000 genomes]
rs302981	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs302985	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs303001	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs303002	0.86[ASN][1000 genomes]
rs303003	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303005	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs303010	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs303011	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs303012	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55851821	0.86[ASN][1000 genomes]
rs6908916	0.86[ASN][1000 genomes]
rs73386265	0.86[ASN][1000 genomes]
rs7740534	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461103	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9654578	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs416030	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25057600-25080400	Weak transcription	Thymus	Thymus
2	chr6:25063200-25079200	Weak transcription	Ovary	ovary
3	chr6:25067400-25080400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:25067600-25084600	Weak transcription	HSMMtube	muscle
5	chr6:25069800-25084000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:25070800-25071200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:25070800-25071200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:25070800-25071200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:25070800-25071200	Active TSS	Primary B cells from cord blood	blood
10	chr6:25070800-25071200	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr6:25070800-25071200	Enhancers	Primary T cells fromperipheralblood	blood
12	chr6:25070800-25071200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr6:25070800-25071200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:25070800-25071200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:25070800-25071200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr6:25070800-25071200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr6:25070800-25071200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:25070800-25071200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:25070800-25071200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:25070800-25071200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:25070800-25071200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:25070800-25071200	Enhancers	Adipose Nuclei	Adipose
23	chr6:25070800-25071200	Enhancers	Brain Anterior Caudate	brain
24	chr6:25070800-25071200	Enhancers	Colonic Mucosa	Colon
25	chr6:25070800-25071200	Enhancers	Fetal Muscle Leg	muscle
26	chr6:25070800-25071200	Enhancers	Placenta	Placenta
27	chr6:25070800-25071200	Enhancers	Fetal Thymus	thymus
28	chr6:25070800-25071200	Flanking Active TSS	Dnd41	blood
29	chr6:25070800-25071200	Active TSS	GM12878-XiMat	blood
30	chr6:25070800-25071200	Enhancers	Hela-S3	cervix
31	chr6:25070800-25071200	Enhancers	Osteobl	bone
32	chr6:25070800-25071400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:25070800-25071400	Enhancers	Liver	Liver
34	chr6:25070800-25071600	Enhancers	Primary T cells from cord blood	blood
35	chr6:25071000-25071200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr6:25071000-25071200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr6:25071000-25071400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr6:25071000-25071400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr6:25071000-25071600	Enhancers	Brain Hippocampus Middle	brain
40	chr6:25071000-25080400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:25071000-25084400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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