Variant report

Variant	rs28415349
Chromosome Location	chr15:52643230-52643231
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52586418..52589137-chr15:52642806..52644960,2	MCF-7	breast:
2	chr15:52642497..52646908-chr15:52859838..52862165,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10518688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1108808	1.00[EUR][1000 genomes]
rs12101973	1.00[EUR][1000 genomes]
rs13329278	1.00[EUR][1000 genomes]
rs13329402	1.00[EUR][1000 genomes]
rs13329417	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13329500	1.00[EUR][1000 genomes]
rs16964891	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964903	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964910	1.00[EUR][1000 genomes]
rs16964915	1.00[EUR][1000 genomes]
rs16964919	1.00[EUR][1000 genomes]
rs16964921	1.00[EUR][1000 genomes]
rs16964924	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964927	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964928	1.00[EUR][1000 genomes]
rs16964935	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16964944	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16964952	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1724577	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2414137	1.00[EUR][1000 genomes]
rs2414138	1.00[EUR][1000 genomes]
rs2600903	0.93[ASN][1000 genomes]
rs2600904	0.93[ASN][1000 genomes]
rs28366864	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28367336	1.00[EUR][1000 genomes]
rs28367508	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28374631	1.00[EUR][1000 genomes]
rs28409636	1.00[EUR][1000 genomes]
rs28409760	1.00[EUR][1000 genomes]
rs28415069	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28415472	0.80[ASN][1000 genomes]
rs28421476	0.80[ASN][1000 genomes]
rs28426997	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28444393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28462026	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28475475	1.00[EUR][1000 genomes]
rs28479614	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28480975	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485251	0.80[ASN][1000 genomes]
rs28488423	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28496242	1.00[EUR][1000 genomes]
rs28499517	0.80[ASN][1000 genomes]
rs28503750	1.00[EUR][1000 genomes]
rs28508266	1.00[EUR][1000 genomes]
rs28514341	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515624	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532168	1.00[EUR][1000 genomes]
rs28534436	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28538563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28552981	1.00[EUR][1000 genomes]
rs28556657	1.00[EUR][1000 genomes]
rs28564655	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28590330	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28594692	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28605633	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613360	0.80[ASN][1000 genomes]
rs28618215	0.93[ASN][1000 genomes]
rs28633243	1.00[EUR][1000 genomes]
rs28638475	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28649737	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650960	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28653534	1.00[EUR][1000 genomes]
rs28655190	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28660682	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661501	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663524	0.80[ASN][1000 genomes]
rs28669685	0.93[ASN][1000 genomes]
rs28682547	0.80[ASN][1000 genomes]
rs28693941	1.00[EUR][1000 genomes]
rs28697879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729511	0.80[ASN][1000 genomes]
rs28735959	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28756182	1.00[EUR][1000 genomes]
rs4499185	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624108	1.00[EUR][1000 genomes]
rs4776042	0.93[ASN][1000 genomes]
rs4987194	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57864537	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58029714	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58812575	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7163569	0.93[ASN][1000 genomes]
rs7164722	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7164872	1.00[EUR][1000 genomes]
rs7166034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7167181	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167680	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167890	0.82[ASN][1000 genomes]
rs7167916	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7168076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168251	1.00[EUR][1000 genomes]
rs7169104	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169346	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170622	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7179156	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7182148	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73408408	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408415	1.00[EUR][1000 genomes]
rs73408465	1.00[EUR][1000 genomes]
rs73408469	1.00[EUR][1000 genomes]
rs73408478	1.00[EUR][1000 genomes]
rs73410713	1.00[EUR][1000 genomes]
rs73410715	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410759	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs744501	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8023623	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8024412	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024624	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027637	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027777	1.00[EUR][1000 genomes]
rs8035199	1.00[EUR][1000 genomes]
rs8040369	1.00[EUR][1000 genomes]
rs8041819	1.00[EUR][1000 genomes]
rs8042235	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042245	1.00[ASN][1000 genomes]
rs876549	1.00[EUR][1000 genomes]
rs9744852	1.00[EUR][1000 genomes]
rs9920195	0.80[ASN][1000 genomes]
rs9920739	1.00[EUR][1000 genomes]
rs9920749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][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	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
5	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
7	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:52611800-52675800	Weak transcription	Gastric	stomach
9	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
10	chr15:52614800-52653200	Weak transcription	Colonic Mucosa	Colon
11	chr15:52620000-52652200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:52620600-52659200	Weak transcription	Fetal Lung	lung
13	chr15:52621200-52666600	Weak transcription	Fetal Brain Male	brain
14	chr15:52621800-52662200	Weak transcription	Psoas Muscle	Psoas
15	chr15:52623800-52644200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr15:52627000-52646600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:52631600-52679200	Weak transcription	Fetal Intestine Small	intestine
19	chr15:52632600-52643400	Weak transcription	Lung	lung
20	chr15:52632600-52644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:52632600-52670400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:52632800-52657400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:52632800-52662200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:52633000-52643800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr15:52633600-52645400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:52633600-52662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:52635200-52648200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr15:52636000-52643400	Weak transcription	Right Atrium	heart
29	chr15:52638000-52671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:52638200-52645800	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr15:52639400-52644600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:52640200-52644600	Strong transcription	GM12878-XiMat	blood
33	chr15:52640200-52646200	Strong transcription	Brain Cingulate Gyrus	brain
34	chr15:52640200-52646200	Strong transcription	Fetal Brain Female	brain
35	chr15:52640200-52646400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:52640200-52646600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:52640200-52647000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:52640200-52647600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr15:52640200-52655000	Weak transcription	Liver	Liver
40	chr15:52640400-52643800	Strong transcription	Adipose Nuclei	Adipose
41	chr15:52640400-52646200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:52640400-52646600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:52640400-52648400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr15:52640600-52646200	Strong transcription	Brain Anterior Caudate	brain
45	chr15:52640600-52646200	Strong transcription	Brain Hippocampus Middle	brain
46	chr15:52640600-52648200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:52640600-52666600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:52641200-52644600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:52641200-52644600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:52641200-52645800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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