Variant report

Variant	rs2516578
Chromosome Location	chr6:25128781-25128782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25122897..25125650-chr6:25128706..25130794,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1046141	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1046142	0.87[AFR][1000 genomes]
rs1128826	0.87[AFR][1000 genomes]
rs1128827	0.85[AFR][1000 genomes]
rs12332924	0.92[AFR][1000 genomes]
rs12333217	0.85[AFR][1000 genomes]
rs12333219	0.85[AFR][1000 genomes]
rs12333222	0.85[AFR][1000 genomes]
rs12333327	0.87[AFR][1000 genomes]
rs16890067	0.87[AFR][1000 genomes]
rs16890087	0.87[AFR][1000 genomes]
rs16890100	0.91[AFR][1000 genomes]
rs2044553	0.82[AFR][1000 genomes]
rs2516576	0.92[AFR][1000 genomes]
rs4538700	0.88[AFR][1000 genomes]
rs6456647	0.89[AFR][1000 genomes]
rs6905460	0.87[AFR][1000 genomes]
rs6905554	0.92[AFR][1000 genomes]
rs6905624	0.87[AFR][1000 genomes]
rs6906421	0.92[AFR][1000 genomes]
rs6913324	0.87[AFR][1000 genomes]
rs6913346	0.86[AFR][1000 genomes]
rs6915329	0.87[AFR][1000 genomes]
rs6925889	0.87[AFR][1000 genomes]
rs6926671	0.90[AFR][1000 genomes]
rs7740848	0.87[AFR][1000 genomes]
rs7745550	0.87[AFR][1000 genomes]
rs7745609	0.87[AFR][1000 genomes]
rs7755584	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7756507	0.85[AFR][1000 genomes]
rs7762804	0.91[AFR][1000 genomes]
rs7773107	0.87[AFR][1000 genomes]
rs7774557	0.87[AFR][1000 genomes]
rs916537	0.92[AFR][1000 genomes]
rs916538	0.92[AFR][1000 genomes]
rs916539	0.92[AFR][1000 genomes]
rs9461101	0.85[AFR][1000 genomes]
rs9461104	0.92[AFR][1000 genomes]
rs9461106	0.89[AFR][1000 genomes]
rs9467388	0.94[AFR][1000 genomes]
rs9467394	0.85[AFR][1000 genomes]
rs9467395	0.85[AFR][1000 genomes]
rs9467396	0.85[AFR][1000 genomes]
rs9467398	0.85[AFR][1000 genomes]
rs9467400	0.85[AFR][1000 genomes]
rs9467401	0.83[AFR][1000 genomes]
rs9467403	0.87[AFR][1000 genomes]
rs9467404	0.87[AFR][1000 genomes]
rs9467405	0.87[AFR][1000 genomes]
rs9467406	0.87[AFR][1000 genomes]
rs9467407	0.94[AFR][1000 genomes]
rs9467408	0.87[AFR][1000 genomes]
rs9467409	0.87[AFR][1000 genomes]
rs9467410	0.87[AFR][1000 genomes]
rs9467411	0.92[AFR][1000 genomes]

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	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
4	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
2	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr6:25110800-25133400	Weak transcription	Aorta	Aorta
4	chr6:25113000-25136800	Weak transcription	Osteobl	bone
5	chr6:25113600-25132800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:25114000-25130600	Weak transcription	Fetal Lung	lung
7	chr6:25116000-25137000	Weak transcription	Lung	lung
8	chr6:25120600-25129800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:25121000-25129800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:25122000-25131600	Strong transcription	Fetal Thymus	thymus
11	chr6:25122600-25132000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:25122600-25133800	Weak transcription	NHDF-Ad	bronchial
13	chr6:25122600-25137000	Weak transcription	Colonic Mucosa	Colon
14	chr6:25122600-25137000	Weak transcription	HSMM	muscle
15	chr6:25122800-25129400	Weak transcription	Ovary	ovary
16	chr6:25122800-25137000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:25123200-25130800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:25123600-25136600	Weak transcription	HSMMtube	muscle
19	chr6:25123800-25129400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:25123800-25136800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:25123800-25138400	Weak transcription	Pancreas	Pancrea
22	chr6:25124200-25129000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:25124400-25138200	Weak transcription	Spleen	Spleen
24	chr6:25125200-25130800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:25125400-25130000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr6:25125400-25130400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:25125400-25130400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:25126200-25130800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:25126200-25133000	Weak transcription	Primary B cells from cord blood	blood
30	chr6:25126200-25133200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:25126200-25136400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:25126400-25130800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:25126400-25131000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:25126400-25132000	Weak transcription	GM12878-XiMat	blood
35	chr6:25126400-25133200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:25126400-25133400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:25126400-25135400	Weak transcription	Thymus	Thymus
38	chr6:25126400-25136800	Weak transcription	Liver	Liver
39	chr6:25126800-25130800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:25127000-25129600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:25127400-25129600	Strong transcription	Primary T cells from cord blood	blood
42	chr6:25127600-25128800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr6:25127800-25128800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
44	chr6:25127800-25129000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr6:25127800-25129000	Strong transcription	Left Ventricle	heart
46	chr6:25127800-25129000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr6:25127800-25129400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:25127800-25129400	Genic enhancers	Dnd41	blood
49	chr6:25128000-25129600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr6:25128000-25130000	Strong transcription	Primary hematopoietic stem cells	blood

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