Variant report

Variant	rs2680348
Chromosome Location	chr15:73562532-73562533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73556714..73560483-chr15:73561340..73564858,6	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1017809	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1029	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11853109	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11856383	0.82[EUR][1000 genomes]
rs11856433	0.82[EUR][1000 genomes]
rs11856466	0.82[EUR][1000 genomes]
rs11857053	0.82[EUR][1000 genomes]
rs12101540	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12101734	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13329282	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1382780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1648248	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1678245	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1714529	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1714530	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1714532	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1812363	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1842164	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1895842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979410	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2169952	0.82[EUR][1000 genomes]
rs2254390	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2254818	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619259	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2623990	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2623994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2623996	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2624002	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2660823	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2680347	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2680351	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28547177	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28582318	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28676873	0.82[EUR][1000 genomes]
rs28808999	0.82[EUR][1000 genomes]
rs28828370	0.82[EUR][1000 genomes]
rs4238459	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4287530	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4325518	0.82[EUR][1000 genomes]
rs4635304	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4776626	0.82[EUR][1000 genomes]
rs4777584	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs490567	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs492448	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs514632	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs524457	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs533460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs550212	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55969660	0.82[EUR][1000 genomes]
rs57453823	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs576414	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6495054	0.82[EUR][1000 genomes]
rs7176908	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7180017	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7403367	0.82[EUR][1000 genomes]
rs7497831	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8031718	0.82[EUR][1000 genomes]
rs8035717	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8038411	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs899480	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9920152	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9920459	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9920675	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73520600-73579600	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:73523000-73572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:73527000-73579400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:73535200-73588000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:73536200-73602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:73536400-73566600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:73537600-73572200	Weak transcription	Fetal Heart	heart
8	chr15:73538000-73593400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:73538200-73562600	Strong transcription	Fetal Intestine Large	intestine
10	chr15:73540000-73565400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:73540000-73584800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:73543000-73567400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr15:73543400-73562800	Weak transcription	Stomach Mucosa	stomach
14	chr15:73544400-73583000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:73546800-73563000	Weak transcription	Right Ventricle	heart
16	chr15:73546800-73583000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr15:73546800-73588600	Weak transcription	Spleen	Spleen
18	chr15:73547600-73576600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr15:73547800-73584600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:73548200-73575000	Weak transcription	Gastric	stomach
21	chr15:73548200-73575200	Weak transcription	Pancreas	Pancrea
22	chr15:73548200-73575600	Weak transcription	Esophagus	oesophagus
23	chr15:73549200-73562600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:73549200-73565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:73549200-73565400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:73549200-73575200	Weak transcription	Brain Germinal Matrix	brain
27	chr15:73549200-73575200	Weak transcription	Lung	lung
28	chr15:73550800-73581400	Weak transcription	HMEC	breast
29	chr15:73551600-73565600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr15:73552000-73577800	Weak transcription	Psoas Muscle	Psoas
31	chr15:73552400-73588200	Weak transcription	Hela-S3	cervix
32	chr15:73552800-73562600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:73552800-73598400	Weak transcription	Small Intestine	intestine
34	chr15:73553200-73562800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:73553800-73581200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr15:73555000-73570600	Weak transcription	Liver	Liver
37	chr15:73555200-73575600	Weak transcription	Colonic Mucosa	Colon
38	chr15:73557800-73564800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:73557800-73567800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:73558600-73562600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:73558600-73564000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:73558800-73563800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:73558800-73565000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:73559200-73562600	Weak transcription	Fetal Brain Male	brain
45	chr15:73559200-73562600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr15:73559200-73566200	Weak transcription	Ovary	ovary
47	chr15:73559400-73562600	Weak transcription	Brain Anterior Caudate	brain
48	chr15:73559600-73562800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr15:73559600-73563800	Weak transcription	Fetal Intestine Small	intestine
50	chr15:73559600-73564800	Weak transcription	Fetal Stomach	stomach

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