Variant report

Variant	rs28744617
Chromosome Location	chr15:42981022-42981023
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: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10162939	0.86[EUR][1000 genomes]
rs10400824	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1197548	0.85[EUR][1000 genomes]
rs1197549	0.85[EUR][1000 genomes]
rs1197550	0.86[EUR][1000 genomes]
rs1197551	0.86[EUR][1000 genomes]
rs12102055	0.81[EUR][1000 genomes]
rs12905385	0.81[AFR][1000 genomes]
rs16957020	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16957168	0.83[ASN][1000 genomes]
rs1705356	0.86[EUR][1000 genomes]
rs1995939	0.81[EUR][1000 genomes]
rs2136899	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2136900	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2175370	0.86[ASN][1000 genomes]
rs2305084	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2412740	0.81[EUR][1000 genomes]
rs28479391	0.81[EUR][1000 genomes]
rs28498538	0.88[ASN][1000 genomes]
rs28562951	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28620320	0.83[ASN][1000 genomes]
rs28664781	0.81[ASN][1000 genomes]
rs28798437	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28811114	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28823029	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3099758	0.85[EUR][1000 genomes]
rs3199486	0.81[EUR][1000 genomes]
rs34603230	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3742993	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4545789	0.81[AFR][1000 genomes]
rs4924690	0.87[EUR][1000 genomes]
rs4924691	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4924694	0.83[ASN][1000 genomes]
rs623271	0.85[EUR][1000 genomes]
rs6493059	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493063	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6493066	0.81[ASN][1000 genomes]
rs7163030	0.87[EUR][1000 genomes]
rs7167392	0.86[ASN][1000 genomes]
rs7169202	0.88[EUR][1000 genomes]
rs7175582	0.84[EUR][1000 genomes]
rs7176860	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7182141	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8024902	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs8039711	0.88[ASN][1000 genomes]
rs8043472	0.87[EUR][1000 genomes]
rs9269	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9783713	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9919994	0.83[EUR][1000 genomes]
rs9920163	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][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	chr15:42965000-42982200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:42966000-42992800	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:42966400-42988400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:42966400-42988600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:42966600-42982400	Strong transcription	Fetal Brain Female	brain
21	chr15:42966600-42982800	Strong transcription	Primary hematopoietic stem cells	blood
22	chr15:42966600-42988000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:42966600-42989200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:42966800-42987600	Strong transcription	Aorta	Aorta
25	chr15:42968400-42992200	Weak transcription	Fetal Brain Male	brain
26	chr15:42968600-42996800	Weak transcription	Liver	Liver
27	chr15:42968600-42999000	Weak transcription	HUVEC	blood vessel
28	chr15:42969400-42988400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:42970200-42983400	Weak transcription	K562	blood
30	chr15:42970600-42990200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:42970800-42986200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr15:42971400-42992600	Strong transcription	Adipose Nuclei	Adipose
33	chr15:42971600-42992400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:42972600-42983600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:42973200-42985600	Strong transcription	Rectal Smooth Muscle	rectum
36	chr15:42973200-42991200	Strong transcription	Brain Germinal Matrix	brain
37	chr15:42973400-42987600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:42973600-42982200	Strong transcription	Right Ventricle	heart
39	chr15:42973600-42988400	Strong transcription	Lung	lung
40	chr15:42973600-42989000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:42973600-42992600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:42974000-42982200	Strong transcription	Brain Hippocampus Middle	brain
43	chr15:42974400-42989200	Strong transcription	Left Ventricle	heart
44	chr15:42975200-42983000	Weak transcription	Fetal Thymus	thymus
45	chr15:42975200-42983000	Weak transcription	HSMMtube	muscle
46	chr15:42975200-42984200	Weak transcription	Colonic Mucosa	Colon
47	chr15:42975600-43011400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:42975800-42981600	Strong transcription	NHDF-Ad	bronchial
49	chr15:42976400-42982400	Strong transcription	Placenta	Placenta
50	chr15:42976600-42984600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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