Variant report

Variant	rs2493330
Chromosome Location	chr6:24898195-24898196
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2255339	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474149	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2747680	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2747681	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2747682	0.85[ASN][1000 genomes]
rs2817714	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2817721	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2817730	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2817750	0.87[EUR][1000 genomes]
rs2817751	0.83[ASN][1000 genomes]
rs9356948	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358807	0.86[EUR][1000 genomes];0.96[ASN][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	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	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24876000-24901800	Weak transcription	Spleen	Spleen
2	chr6:24878400-24899800	Weak transcription	Thymus	Thymus
3	chr6:24881200-24898400	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr6:24882400-24904000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:24882600-24899200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:24884000-24908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:24884200-24899800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:24887000-24900000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:24889000-24898600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:24889400-24899800	Weak transcription	Brain Anterior Caudate	brain
11	chr6:24889600-24899600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:24889600-24900000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:24890600-24899200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:24890600-24900800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:24891000-24902800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:24891600-24901400	Weak transcription	GM12878-XiMat	blood
17	chr6:24891600-24901800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:24891600-24908400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:24892000-24900200	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:24892600-24898400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:24894800-24900000	Weak transcription	Fetal Thymus	thymus
22	chr6:24895800-24898400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:24896400-24902600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
24	chr6:24896400-24908600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr6:24896600-24899400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr6:24897000-24899800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:24897200-24900000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr6:24897400-24899800	Genic enhancers	Primary T cells from cord blood	blood
29	chr6:24897400-24901200	Enhancers	Fetal Brain Male	brain
30	chr6:24897400-24901400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr6:24897400-24903800	Genic enhancers	Primary B cells from cord blood	blood
32	chr6:24897400-24904800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:24897400-24907600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:24897400-24909600	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr6:24897600-24899400	Enhancers	Brain Germinal Matrix	brain
36	chr6:24897800-24898800	Weak transcription	NHDF-Ad	bronchial
37	chr6:24897800-24899400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr6:24897800-24899800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:24897800-24899800	Weak transcription	Fetal Heart	heart
40	chr6:24897800-24900000	Weak transcription	Psoas Muscle	Psoas
41	chr6:24897800-24900000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:24897800-24901400	Weak transcription	HSMM	muscle
43	chr6:24898000-24898200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:24898000-24898200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr6:24898000-24898400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:24898000-24899200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:24898000-24899600	Weak transcription	Fetal Brain Female	brain
48	chr6:24898000-24899600	Weak transcription	HSMMtube	muscle
49	chr6:24898000-24900400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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