Variant report

Variant	rs4712876
Chromosome Location	chr6:24995957-24995958
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10946739	0.93[EUR][1000 genomes]
rs10946740	0.82[EUR][1000 genomes]
rs12192232	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12194111	0.93[EUR][1000 genomes]
rs12205717	0.90[EUR][1000 genomes]
rs1410686	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1410687	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2149452	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2209932	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2894032	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712870	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712872	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62401116	0.93[EUR][1000 genomes]
rs6456641	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6935286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740315	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7765689	0.83[EUR][1000 genomes]
rs7765852	0.83[EUR][1000 genomes]
rs7768143	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295639	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9295640	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295641	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9358815	0.86[ASN][1000 genomes]
rs9358816	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366591	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9393600	0.82[JPT][hapmap];0.82[EUR][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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24986000-24996600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:24986600-24996600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:24987600-25000200	Weak transcription	Lung	lung
4	chr6:24992200-24996600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:24992200-24996600	Weak transcription	Fetal Thymus	thymus
6	chr6:24992200-24996600	Weak transcription	Stomach Mucosa	stomach
7	chr6:24992200-24998000	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:24992200-25006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:24992400-24996600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:24992600-24996400	Weak transcription	Hela-S3	cervix
11	chr6:24992600-24996600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:24992600-24996800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:24992600-25000000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:24992800-24996400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:24992800-24996400	Weak transcription	Primary T cells from cord blood	blood
16	chr6:24992800-24996400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:24992800-24996600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:24992800-24996600	Weak transcription	Dnd41	blood
19	chr6:24992800-24996800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:24992800-24997400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:24993000-24997000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:24994000-24996600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:24994600-24996600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:24994600-24996800	Enhancers	Primary B cells from cord blood	blood
25	chr6:24994800-24996000	Enhancers	Primary T cells fromperipheralblood	blood
26	chr6:24994800-24996400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:24995200-24996400	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr6:24995200-25000600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr6:24995400-24996200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:24995400-24996400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr6:24995600-24996400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:24995600-24996600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:24995600-24996600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:24995600-24996600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr6:24995600-24996800	Enhancers	Placenta	Placenta
36	chr6:24995600-24997800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:24995600-24998400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr6:24995600-25006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:24995800-24996200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:24995800-24996400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:24995800-24996600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:24995800-25006400	Weak transcription	Thymus	Thymus

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