Variant report

Variant	rs10946740
Chromosome Location	chr6:24999967-24999968
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10946739	0.81[EUR][1000 genomes]
rs12192232	0.81[EUR][1000 genomes]
rs12194111	0.81[EUR][1000 genomes]
rs4712871	0.81[EUR][1000 genomes]
rs4712872	0.81[EUR][1000 genomes]
rs4712876	0.82[EUR][1000 genomes]
rs62401116	0.81[EUR][1000 genomes]
rs6935286	0.81[EUR][1000 genomes]
rs7753740	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7765689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7768143	0.81[EUR][1000 genomes]
rs9356952	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9366591	0.81[EUR][1000 genomes]
rs9393605	0.92[EUR][1000 genomes];0.88[ASN][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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24987600-25000200	Weak transcription	Lung	lung
2	chr6:24992200-25006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:24992600-25000000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:24995200-25000600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:24995600-25006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:24995800-25006400	Weak transcription	Thymus	Thymus
7	chr6:24996200-25001000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:24996400-25001200	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:24996600-25001200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:24996600-25001200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr6:24997200-25002600	Weak transcription	Adipose Nuclei	Adipose
12	chr6:24997600-25006400	Weak transcription	Hela-S3	cervix
13	chr6:24997800-25000600	Enhancers	GM12878-XiMat	blood
14	chr6:24997800-25016600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:24998200-25000000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:24998200-25000200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:24998200-25002600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:24998200-25004400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:24998200-25006800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:24998200-25009200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:24998400-25000200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr6:24998400-25000200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:24998400-25000200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:24998400-25000400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:24998400-25000800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr6:24998400-25002600	Weak transcription	Primary T cells from cord blood	blood
27	chr6:24998400-25004600	Weak transcription	Fetal Thymus	thymus
28	chr6:24998400-25006400	Weak transcription	Dnd41	blood
29	chr6:24998600-25001200	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr6:24999000-25002600	Weak transcription	Brain Germinal Matrix	brain
31	chr6:24999200-25000600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:24999200-25000600	Enhancers	Spleen	Spleen
33	chr6:24999200-25000600	Enhancers	HMEC	breast
34	chr6:24999200-25001000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:24999200-25001200	Enhancers	NHEK	skin
36	chr6:24999200-25006600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:24999400-25000000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:24999400-25000600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr6:24999400-25001200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:24999400-25002600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:24999800-25000200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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