Variant report

Variant	rs28680600
Chromosome Location	chr15:42979105-42979106
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	chr15:42969516..42971199-chr15:42979000..42981438,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12323990	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12324135	0.87[EUR][1000 genomes]
rs12591415	0.95[ASN][1000 genomes]
rs12592374	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12592573	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594325	0.95[ASN][1000 genomes]
rs12594378	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12594600	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594696	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594699	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12594724	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594725	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594765	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594837	0.98[ASN][1000 genomes]
rs12595722	0.88[ASN][1000 genomes]
rs16957043	0.87[EUR][1000 genomes]
rs16957055	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16957061	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16957063	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16957120	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1915242	0.87[EUR][1000 genomes]
rs1915243	0.87[EUR][1000 genomes]
rs28431056	0.95[ASN][1000 genomes]
rs28437884	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28661826	0.95[ASN][1000 genomes]
rs28699522	0.87[EUR][1000 genomes]
rs28736688	1.00[EUR][1000 genomes]
rs3742992	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742995	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4334272	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56046122	0.95[ASN][1000 genomes]
rs56839966	0.87[EUR][1000 genomes]
rs58237318	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58548142	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60723187	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61747153	0.98[ASN][1000 genomes]
rs7169231	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169238	0.81[ASN][1000 genomes]
rs7178483	1.00[EUR][1000 genomes]
rs73408611	0.87[EUR][1000 genomes]
rs73408619	1.00[EUR][1000 genomes]
rs73410923	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73410927	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410931	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410937	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410940	0.95[ASN][1000 genomes]
rs73410959	0.95[ASN][1000 genomes]
rs73410961	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410969	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410971	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410972	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410973	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410981	0.87[EUR][1000 genomes]
rs8023743	1.00[EUR][1000 genomes]
rs8028365	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8028699	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8033336	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8036733	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8043143	1.00[EUR][1000 genomes]
rs9944270	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv517553	chr15:42970899-43023482	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
2	chr15:42949800-42999200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr15:42950400-42990200	Strong transcription	Fetal Stomach	stomach
4	chr15:42951000-42995000	Strong transcription	Fetal Muscle Trunk	muscle
5	chr15:42952600-42995600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:42952800-42996000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:42953400-42992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:42954600-42986200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:42954800-42983000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:42955000-42990200	Strong transcription	Fetal Muscle Leg	muscle
11	chr15:42960000-42981800	Strong transcription	Primary T cells from cord blood	blood
12	chr15:42961200-42989200	Strong transcription	Ovary	ovary
13	chr15:42961400-42990800	Strong transcription	Colon Smooth Muscle	Colon
14	chr15:42961600-42989200	Weak transcription	Pancreas	Pancrea
15	chr15:42964200-42982400	Weak transcription	A549	lung
16	chr15:42964600-42979200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:42965000-42982200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:42966000-42992800	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:42966400-42988400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:42966400-42988600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:42966600-42979400	Strong transcription	Spleen	Spleen
22	chr15:42966600-42979800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:42966600-42982400	Strong transcription	Fetal Brain Female	brain
24	chr15:42966600-42982800	Strong transcription	Primary hematopoietic stem cells	blood
25	chr15:42966600-42988000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:42966600-42989200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:42966800-42987600	Strong transcription	Aorta	Aorta
28	chr15:42968400-42992200	Weak transcription	Fetal Brain Male	brain
29	chr15:42968600-42996800	Weak transcription	Liver	Liver
30	chr15:42968600-42999000	Weak transcription	HUVEC	blood vessel
31	chr15:42969400-42988400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:42970200-42983400	Weak transcription	K562	blood
33	chr15:42970400-42979800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:42970600-42990200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:42970800-42986200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr15:42971400-42992600	Strong transcription	Adipose Nuclei	Adipose
37	chr15:42971600-42992400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:42972600-42983600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr15:42973200-42979800	Weak transcription	NHEK	skin
40	chr15:42973200-42981000	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr15:42973200-42985600	Strong transcription	Rectal Smooth Muscle	rectum
42	chr15:42973200-42991200	Strong transcription	Brain Germinal Matrix	brain
43	chr15:42973400-42979400	Strong transcription	Brain Cingulate Gyrus	brain
44	chr15:42973400-42987600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:42973600-42979200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr15:42973600-42979400	Strong transcription	Brain Substantia Nigra	brain
47	chr15:42973600-42979600	Strong transcription	Brain Angular Gyrus	brain
48	chr15:42973600-42979800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr15:42973600-42980000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:42973600-42982200	Strong transcription	Right Ventricle	heart

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