Variant report

Variant	rs2254390
Chromosome Location	chr15:73547716-73547717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HCN4-1	chr15:73547675-73547875	ENSG00000259528.1

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1017809	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1029	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1038136	0.82[EUR][1000 genomes]
rs11852881	0.82[EUR][1000 genomes]
rs11853109	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11856383	0.85[EUR][1000 genomes]
rs11856433	0.85[EUR][1000 genomes]
rs11856466	0.85[EUR][1000 genomes]
rs11857053	0.85[EUR][1000 genomes]
rs12101540	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12101734	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13329282	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1382780	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1648248	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1678245	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16957661	0.82[EUR][1000 genomes]
rs1714529	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1714530	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1714532	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1812363	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1842164	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1895842	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1979410	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2169952	0.85[EUR][1000 genomes]
rs2254818	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2619259	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2623990	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2623994	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2623996	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2624002	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2660823	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2680347	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2680348	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2680350	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2680351	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28547177	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28572029	0.82[EUR][1000 genomes]
rs28582318	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28676873	0.85[EUR][1000 genomes]
rs28808999	0.85[EUR][1000 genomes]
rs28828370	0.85[EUR][1000 genomes]
rs4238459	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4287530	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4325518	0.85[EUR][1000 genomes]
rs4539561	0.82[EUR][1000 genomes]
rs4635304	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4776626	0.85[EUR][1000 genomes]
rs4777584	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs490567	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs492448	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs514632	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs524457	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs533460	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs550212	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs55969660	0.85[EUR][1000 genomes]
rs57453823	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs576414	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6495054	0.85[EUR][1000 genomes]
rs7176908	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7180017	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73438015	0.80[EUR][1000 genomes]
rs7403367	0.85[EUR][1000 genomes]
rs7497831	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8031718	0.85[EUR][1000 genomes]
rs8034243	0.82[EUR][1000 genomes]
rs8035717	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8038411	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs899480	0.88[LWK][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9920152	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9920459	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9920675	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73518800-73547800	Weak transcription	Left Ventricle	heart
2	chr15:73520400-73562400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:73520600-73579600	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:73523000-73572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr15:73523200-73547800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:73525000-73548800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:73525600-73547800	Weak transcription	Gastric	stomach
8	chr15:73527000-73579400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr15:73527400-73551600	Weak transcription	Small Intestine	intestine
10	chr15:73527600-73562400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:73529000-73552600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:73530800-73551200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:73535200-73588000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:73536000-73550800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr15:73536200-73602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:73536400-73559200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr15:73536400-73566600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:73536800-73562400	Weak transcription	A549	lung
19	chr15:73537000-73547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:73537200-73547800	Weak transcription	Fetal Brain Female	brain
21	chr15:73537600-73572200	Weak transcription	Fetal Heart	heart
22	chr15:73538000-73593400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:73538200-73562600	Strong transcription	Fetal Intestine Large	intestine
24	chr15:73540000-73552000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:73540000-73565400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:73540000-73584800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:73540800-73562400	Weak transcription	HepG2	liver
28	chr15:73541600-73550200	Weak transcription	Colonic Mucosa	Colon
29	chr15:73542400-73547800	Weak transcription	Brain Substantia Nigra	brain
30	chr15:73542600-73547800	Weak transcription	Brain Germinal Matrix	brain
31	chr15:73543000-73567400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr15:73543400-73552200	Strong transcription	Fetal Intestine Small	intestine
33	chr15:73543400-73562800	Weak transcription	Stomach Mucosa	stomach
34	chr15:73543600-73553600	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:73543800-73555400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:73544000-73557800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:73544200-73547800	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr15:73544200-73555400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:73544400-73583000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:73544600-73555400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:73544800-73555400	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:73545400-73550400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:73545600-73555600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:73545800-73549200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:73546000-73548400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:73546000-73550400	Strong transcription	Brain Anterior Caudate	brain
47	chr15:73546000-73554000	Strong transcription	Brain Hippocampus Middle	brain
48	chr15:73546000-73555000	Strong transcription	Liver	Liver
49	chr15:73546200-73548200	Strong transcription	Esophagus	oesophagus
50	chr15:73546200-73548600	Strong transcription	Aorta	Aorta

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