Variant report

Variant	rs7758438
Chromosome Location	chr6:24905909-24905910
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	chr6:24905708..24907568-chr6:24908173..24910431,2	K562	blood:
2	chr6:24904971..24907237-chr6:24911875..24914171,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP3-369A17.5.1-3	chr6:24905536-24906044	l_3137_chr6:24904923-24907159_testes

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17839854	0.90[AFR][1000 genomes]
rs45617645	0.90[AFR][1000 genomes]
rs60985329	0.85[AFR][1000 genomes]
rs6913594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6914059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6936710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73398433	0.85[AFR][1000 genomes]
rs73398436	0.85[AFR][1000 genomes]
rs73398461	0.90[AFR][1000 genomes]
rs73398472	0.90[AFR][1000 genomes]
rs73398481	0.90[AFR][1000 genomes]
rs73400424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73400425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73400436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73400437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73400441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73400452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7773196	0.86[EUR][1000 genomes]
rs7773553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7776271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24884000-24908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:24891600-24908400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:24896400-24908600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr6:24897400-24907600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:24897400-24909600	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr6:24899000-24908200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:24899800-24909600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:24900000-24906000	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr6:24900000-24909000	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr6:24900200-24909800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:24900400-24907800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:24900400-24908200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:24900400-24908200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:24900400-24908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:24900600-24907200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr6:24900600-24907600	Weak transcription	Fetal Heart	heart
17	chr6:24901000-24908800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:24901800-24907800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:24901800-24908000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:24901800-24908800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:24902000-24907800	Weak transcription	GM12878-XiMat	blood
22	chr6:24902200-24907600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:24902200-24909400	Weak transcription	Left Ventricle	heart
24	chr6:24902400-24907800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:24903200-24906400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr6:24903200-24906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:24903600-24906400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr6:24903600-24908600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:24903600-24908800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:24903800-24906200	Strong transcription	Primary B cells from cord blood	blood
31	chr6:24904200-24907800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:24904200-24908200	Weak transcription	Dnd41	blood
33	chr6:24904400-24906000	Weak transcription	Psoas Muscle	Psoas
34	chr6:24904400-24906000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr6:24904400-24909000	Weak transcription	HSMM	muscle
36	chr6:24904800-24906000	Genic enhancers	HSMMtube	muscle
37	chr6:24904800-24906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:24904800-24907200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:24904800-24908000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:24904800-24908200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:24905000-24908800	Weak transcription	Spleen	Spleen
42	chr6:24905000-24910800	Weak transcription	Aorta	Aorta
43	chr6:24905200-24908000	Weak transcription	Thymus	Thymus
44	chr6:24905200-24908600	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr6:24905400-24906600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:24905400-24906600	Enhancers	NHDF-Ad	bronchial
47	chr6:24905400-24908000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
48	chr6:24905400-24908200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr6:24905600-24906200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:24905600-24906400	Enhancers	Brain Anterior Caudate	brain

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