Variant report

Variant	rs10946739
Chromosome Location	chr6:24993127-24993128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10806997	1.00[YRI][hapmap]
rs10946737	0.83[EUR][1000 genomes]
rs10946740	0.81[EUR][1000 genomes]
rs10946742	1.00[YRI][hapmap]
rs11758900	0.81[ASN][1000 genomes]
rs12192232	0.95[EUR][1000 genomes]
rs12194111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12205717	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1410686	0.82[EUR][1000 genomes]
rs1410687	0.89[EUR][1000 genomes]
rs2149452	0.86[EUR][1000 genomes]
rs2209932	0.86[EUR][1000 genomes]
rs2894032	0.87[EUR][1000 genomes]
rs4712870	0.93[EUR][1000 genomes]
rs4712871	0.88[CEU][hapmap];0.92[CHD][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs4712872	0.88[CEU][hapmap];0.88[CHD][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs4712876	0.93[EUR][1000 genomes]
rs62401116	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456641	0.82[EUR][1000 genomes]
rs6900169	0.83[EUR][1000 genomes]
rs6935286	0.95[EUR][1000 genomes]
rs742952	0.82[EUR][1000 genomes]
rs7740315	0.92[EUR][1000 genomes]
rs7753740	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7765689	0.82[EUR][1000 genomes]
rs7765852	0.82[EUR][1000 genomes]
rs7768143	0.95[EUR][1000 genomes]
rs9295639	0.85[EUR][1000 genomes]
rs9295640	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[EUR][1000 genomes]
rs9295641	0.93[EUR][1000 genomes]
rs9358816	0.86[EUR][1000 genomes]
rs9366591	0.92[EUR][1000 genomes]
rs9393600	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	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
5	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
6	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
7	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10946739	ZSCAN16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24984200-24995200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24986000-24996600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:24986400-24995200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:24986400-24995400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:24986600-24996600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:24987600-25000200	Weak transcription	Lung	lung
7	chr6:24990400-24993800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:24992200-24995200	Weak transcription	Thymus	Thymus
9	chr6:24992200-24995600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:24992200-24996600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:24992200-24996600	Weak transcription	Fetal Thymus	thymus
12	chr6:24992200-24996600	Weak transcription	Stomach Mucosa	stomach
13	chr6:24992200-24998000	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:24992200-25006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:24992400-24993600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr6:24992400-24996600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:24992600-24993200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:24992600-24993400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:24992600-24993800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:24992600-24994600	Weak transcription	Primary B cells from cord blood	blood
21	chr6:24992600-24995200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:24992600-24995600	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr6:24992600-24995600	Weak transcription	Fetal Heart	heart
24	chr6:24992600-24995800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:24992600-24996400	Weak transcription	Hela-S3	cervix
26	chr6:24992600-24996600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:24992600-24996800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:24992600-25000000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:24992800-24994600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:24992800-24994800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:24992800-24995200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr6:24992800-24996400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:24992800-24996400	Weak transcription	Primary T cells from cord blood	blood
34	chr6:24992800-24996400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:24992800-24996600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:24992800-24996600	Weak transcription	Dnd41	blood
37	chr6:24992800-24996800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:24992800-24997400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:24993000-24993400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr6:24993000-24995200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:24993000-24997000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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