Variant report

Variant	rs9295642
Chromosome Location	chr6:24997462-24997463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13190691	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs1410688	0.81[CHD][hapmap]
rs16889916	0.83[JPT][hapmap]
rs66827126	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7773555	0.83[ASN][1000 genomes]
rs9467373	0.83[ASN][1000 genomes]
rs9467374	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467375	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9295642	C6orf62	cis	parietal	SCAN
rs9295642	ACOT13	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24987600-25000200	Weak transcription	Lung	lung
2	chr6:24992200-24998000	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:24992200-25006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:24992600-25000000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:24995200-25000600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:24995600-24997800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:24995600-24998400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr6:24995600-25006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:24995800-25006400	Weak transcription	Thymus	Thymus
10	chr6:24996200-25001000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:24996400-24997600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr6:24996400-24997600	Enhancers	Hela-S3	cervix
13	chr6:24996400-24997800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:24996400-24998400	Enhancers	Primary T cells from cord blood	blood
15	chr6:24996400-24998400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr6:24996400-24998600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr6:24996400-24998600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr6:24996400-24999400	Enhancers	Primary hematopoietic stem cells	blood
19	chr6:24996400-24999400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:24996400-25001200	Enhancers	Primary B cells from peripheral blood	blood
21	chr6:24996600-24998200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:24996600-24998200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:24996600-24998200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:24996600-24998200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:24996600-24998400	Enhancers	H1 Cell Line	embryonic stem cell
26	chr6:24996600-24998400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:24996600-24998400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:24996600-24998400	Enhancers	Fetal Thymus	thymus
29	chr6:24996600-24998400	Enhancers	Dnd41	blood
30	chr6:24996600-24999000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr6:24996600-24999200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:24996600-24999200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr6:24996600-24999200	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr6:24996600-25001200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:24996600-25001200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr6:24996800-24997800	Weak transcription	Spleen	Spleen
37	chr6:24996800-24998200	Enhancers	H9 Cell Line	embryonic stem cell
38	chr6:24996800-24998200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr6:24996800-24999000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr6:24997000-24998400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr6:24997000-24999200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:24997200-24997600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:24997200-24998400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr6:24997200-24999200	Enhancers	Primary B cells from cord blood	blood
45	chr6:24997200-25002600	Weak transcription	Adipose Nuclei	Adipose
46	chr6:24997400-24997800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr6:24997400-24998400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr6:24997400-24998400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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