Variant report

Variant	rs2469221
Chromosome Location	chr15:76579664-76579665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76575843..76577535-chr15:76579301..76581844,2	MCF-7	breast:
2	chr15:76579019..76580557-chr15:76600815..76603366,2	K562	blood:
3	chr15:76577736..76580355-chr15:76602966..76605157,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCAPER-4	chr15:76579463-76579945	ncRnaDb_ncrna_FR182241_1

Variant related genes	Relation type
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10220790	1.00[AMR][1000 genomes]
rs12708522	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1533600	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs157764	1.00[AMR][1000 genomes]
rs157765	1.00[AMR][1000 genomes]
rs157767	1.00[AMR][1000 genomes]
rs157774	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs157781	1.00[AMR][1000 genomes]
rs157782	1.00[AMR][1000 genomes]
rs157784	1.00[AMR][1000 genomes]
rs157786	1.00[AMR][1000 genomes]
rs166932	1.00[AMR][1000 genomes]
rs1810347	1.00[AMR][1000 genomes]
rs1814764	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs185860	1.00[AMR][1000 genomes]
rs1875886	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1878877	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs190782	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2037306	1.00[AMR][1000 genomes]
rs2176622	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2244050	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2245180	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2247488	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2250805	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2405329	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2405330	1.00[AMR][1000 genomes]
rs2405332	1.00[AMR][1000 genomes]
rs2456030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456032	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456034	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456035	1.00[AMR][1000 genomes]
rs2456036	1.00[AMR][1000 genomes]
rs2456037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456038	1.00[AMR][1000 genomes]
rs2456039	1.00[AMR][1000 genomes]
rs2456043	0.83[AMR][1000 genomes]
rs2456044	1.00[AMR][1000 genomes]
rs2456056	1.00[AMR][1000 genomes]
rs2456058	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456059	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456077	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2459364	1.00[AMR][1000 genomes]
rs2460141	1.00[AMR][1000 genomes]
rs2460143	1.00[AMR][1000 genomes]
rs2460145	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2460149	1.00[AMR][1000 genomes]
rs2460157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2460159	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469217	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469218	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469219	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469223	1.00[AMR][1000 genomes]
rs2469536	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469537	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469540	1.00[AMR][1000 genomes]
rs2469545	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469546	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469551	1.00[AMR][1000 genomes]
rs2469553	1.00[AMR][1000 genomes]
rs2469571	1.00[AMR][1000 genomes]
rs2469572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2469574	1.00[AMR][1000 genomes]
rs2516308	1.00[AMR][1000 genomes]
rs283788	1.00[AMR][1000 genomes]
rs283790	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs283792	1.00[AMR][1000 genomes]
rs283794	1.00[AMR][1000 genomes]
rs283797	1.00[AMR][1000 genomes]
rs283798	0.83[AMR][1000 genomes]
rs283800	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs284879	1.00[AMR][1000 genomes]
rs284887	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs284888	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs284889	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs284890	1.00[AMR][1000 genomes]
rs284894	0.83[AMR][1000 genomes]
rs284900	1.00[AMR][1000 genomes]
rs2938692	1.00[AMR][1000 genomes]
rs2938693	1.00[AMR][1000 genomes]
rs2938694	0.83[AMR][1000 genomes]
rs2938696	1.00[AMR][1000 genomes]
rs2938698	1.00[AMR][1000 genomes]
rs2944379	1.00[AMR][1000 genomes]
rs2944380	1.00[AMR][1000 genomes]
rs2948702	1.00[AMR][1000 genomes]
rs2956872	1.00[AMR][1000 genomes]
rs2957558	1.00[AMR][1000 genomes]
rs2957608	1.00[AMR][1000 genomes]
rs426225	0.83[AMR][1000 genomes]
rs4886797	1.00[AMR][1000 genomes]
rs542148	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs598011	1.00[AMR][1000 genomes]
rs6495202	1.00[AMR][1000 genomes]
rs7164815	1.00[AMR][1000 genomes]
rs8040818	1.00[AMR][1000 genomes]
rs937731	1.00[AMR][1000 genomes]
rs937734	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76555800-76586000	Weak transcription	Stomach Mucosa	stomach
2	chr15:76556400-76581400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:76556800-76594600	Weak transcription	Esophagus	oesophagus
4	chr15:76557000-76582800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:76558000-76603000	Weak transcription	Aorta	Aorta
6	chr15:76560000-76582400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:76561000-76580400	Strong transcription	Adipose Nuclei	Adipose
8	chr15:76561000-76587600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:76562000-76591600	Weak transcription	Small Intestine	intestine
10	chr15:76562600-76586000	Weak transcription	Brain Angular Gyrus	brain
11	chr15:76562800-76580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:76563000-76581800	Weak transcription	Fetal Brain Male	brain
13	chr15:76563000-76586400	Weak transcription	Fetal Heart	heart
14	chr15:76563200-76590800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:76564200-76580600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:76565200-76581200	Strong transcription	HepG2	liver
17	chr15:76565200-76581400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:76567600-76581800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:76568800-76581600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:76569000-76580600	Strong transcription	Osteobl	bone
21	chr15:76569000-76585200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:76569000-76586400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:76569200-76580400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:76569200-76581400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr15:76569200-76581600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr15:76569400-76579800	Strong transcription	Fetal Lung	lung
27	chr15:76569400-76580400	Strong transcription	Fetal Muscle Leg	muscle
28	chr15:76569400-76583600	Strong transcription	Hela-S3	cervix
29	chr15:76569400-76585000	Strong transcription	Fetal Intestine Large	intestine
30	chr15:76569800-76591600	Weak transcription	Spleen	Spleen
31	chr15:76570000-76580000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:76570800-76581400	Weak transcription	Fetal Brain Female	brain
33	chr15:76571200-76586400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr15:76572000-76580400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:76572000-76581600	Strong transcription	Placenta	Placenta
36	chr15:76572600-76585800	Weak transcription	Brain Anterior Caudate	brain
37	chr15:76573200-76592200	Weak transcription	Fetal Kidney	kidney
38	chr15:76573200-76593200	Weak transcription	Right Ventricle	heart
39	chr15:76573600-76580400	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:76574200-76580400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr15:76574400-76580200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr15:76574600-76580400	Strong transcription	K562	blood
43	chr15:76574600-76585200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:76574800-76582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:76574800-76590600	Weak transcription	Ovary	ovary
46	chr15:76574800-76591600	Weak transcription	Gastric	stomach
47	chr15:76574800-76591600	Weak transcription	Lung	lung
48	chr15:76574800-76601400	Weak transcription	Pancreas	Pancrea
49	chr15:76574800-76602000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:76575000-76586000	Weak transcription	Brain Inferior Temporal Lobe	brain

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