Variant report

Variant	rs72729459
Chromosome Location	chr15:40238027-40238028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40226451..40228182-chr15:40236413..40239026,2	MCF-7	breast:
2	chr15:40227974..40230444-chr15:40236467..40239295,4	K562	blood:
3	chr15:40225075..40228327-chr15:40235171..40238770,3	MCF-7	breast:
4	chr15:40237266..40239005-chr15:40269380..40272206,2	K562	blood:

Variant related genes	Relation type
ENSG00000128829	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10459608	0.89[ASN][1000 genomes]
rs12441486	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1436276	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1436278	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1689605	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16970030	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16970033	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16970098	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16970132	0.87[AMR][1000 genomes]
rs2196470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307105	0.90[EUR][1000 genomes]
rs2307106	0.90[EUR][1000 genomes]
rs2307107	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2640645	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28369403	0.87[AMR][1000 genomes]
rs28619481	0.87[AMR][1000 genomes]
rs35390951	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3765127	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4566130	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs472027	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs479500	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs503671	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs509200	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs510949	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs514152	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs518802	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs536503	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs548091	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66690776	0.82[AMR][1000 genomes]
rs7165105	0.83[AMR][1000 genomes]
rs7170569	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174767	0.90[EUR][1000 genomes]
rs72729462	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729469	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72729490	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72729494	0.87[AMR][1000 genomes]
rs8029465	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8036381	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8036388	0.90[EUR][1000 genomes]
rs9888665	0.87[AMR][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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv832983	chr15:40098766-40248839	Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40227200-40247800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:40227200-40248200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:40227200-40268400	Weak transcription	Esophagus	oesophagus
4	chr15:40227400-40283400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:40227800-40247000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:40227800-40268400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:40228000-40238400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr15:40228200-40323800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:40228600-40239800	Weak transcription	Stomach Mucosa	stomach
10	chr15:40228600-40246000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:40230000-40263000	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:40230200-40255600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:40230400-40240000	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr15:40230400-40261600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:40230600-40252400	Weak transcription	Right Atrium	heart
16	chr15:40230800-40239600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:40230800-40240000	Strong transcription	Fetal Stomach	stomach
18	chr15:40231000-40268400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:40231400-40243400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:40231800-40238800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr15:40231800-40239000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:40231800-40240200	Strong transcription	Fetal Muscle Leg	muscle
23	chr15:40231800-40243400	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr15:40231800-40252600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:40232000-40240000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr15:40232000-40240400	Strong transcription	Primary B cells from cord blood	blood
27	chr15:40232000-40261400	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:40232000-40262600	Strong transcription	Liver	Liver
29	chr15:40232200-40238800	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:40232200-40239000	Strong transcription	HepG2	liver
31	chr15:40232200-40239400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:40232200-40239400	Strong transcription	Fetal Intestine Large	intestine
33	chr15:40232200-40239600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:40232200-40239800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr15:40232200-40240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:40232200-40240000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr15:40232200-40240200	Strong transcription	Fetal Thymus	thymus
38	chr15:40232200-40241600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:40232200-40244600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:40232200-40250200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr15:40232200-40252400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr15:40232400-40238600	Strong transcription	Lung	lung
43	chr15:40232400-40240000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr15:40232400-40252400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr15:40232600-40238600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr15:40232600-40240000	Strong transcription	GM12878-XiMat	blood
47	chr15:40232600-40240400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr15:40232600-40251000	Strong transcription	Left Ventricle	heart
49	chr15:40232600-40251800	Strong transcription	Adipose Nuclei	Adipose
50	chr15:40233000-40239000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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