Variant report

Variant	rs72729462
Chromosome Location	chr15:40243660-40243661
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40226223..40227908-chr15:40241958..40244363,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR176-1	chr15:40243576-40243909	NONHSAT041782

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:39)

rs_ID	r²[population]
rs10459608	0.83[ASN][1000 genomes]
rs12441486	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1436276	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1436278	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689605	0.82[ASN][1000 genomes]
rs16970030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16970033	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970098	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16970132	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2196470	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2307105	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2307106	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2307107	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2640645	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28369403	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28619481	0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35390951	0.84[ASN][1000 genomes]
rs3765127	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4566130	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs472027	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs479500	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs503671	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs509200	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs510949	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs514152	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs518802	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs536503	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs548091	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165105	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7170569	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174767	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72729459	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729469	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729490	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72729494	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8029465	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8036381	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8036388	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9888665	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv974559	chr15:40241861-40243776	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 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	chr15:40228200-40323800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:40228600-40246000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:40230000-40263000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr15:40230200-40255600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:40230400-40261600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:40230600-40252400	Weak transcription	Right Atrium	heart
13	chr15:40231000-40268400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:40231800-40252600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:40232000-40261400	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:40232000-40262600	Strong transcription	Liver	Liver
17	chr15:40232200-40244600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr15:40232200-40250200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:40232200-40252400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:40232400-40252400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr15:40232600-40251000	Strong transcription	Left Ventricle	heart
22	chr15:40232600-40251800	Strong transcription	Adipose Nuclei	Adipose
23	chr15:40233400-40248600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr15:40234800-40244200	Strong transcription	NHEK	skin
25	chr15:40235000-40245000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:40235000-40245400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:40235000-40263000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:40235200-40244200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:40236000-40255400	Strong transcription	Fetal Lung	lung
30	chr15:40236000-40260000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr15:40236400-40244200	Strong transcription	Dnd41	blood
32	chr15:40236600-40245600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:40236600-40303000	Weak transcription	Small Intestine	intestine
34	chr15:40237800-40255600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:40238000-40277800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr15:40238200-40245800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:40238200-40247000	Weak transcription	K562	blood
38	chr15:40238600-40244000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr15:40238600-40268200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr15:40238600-40272200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:40238800-40245600	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:40238800-40247000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr15:40238800-40248600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:40238800-40273200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:40239000-40243800	Weak transcription	HSMMtube	muscle
46	chr15:40239000-40247200	Weak transcription	Fetal Heart	heart
47	chr15:40239200-40245600	Strong transcription	HMEC	breast
48	chr15:40239200-40259600	Weak transcription	Fetal Brain Male	brain
49	chr15:40239400-40244400	Strong transcription	NH-A	brain
50	chr15:40239400-40245600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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