Variant report

Variant	rs10519221
Chromosome Location	chr15:49578574-49578575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49577260..49579059-chr20:45986069..45987868,2	MCF-7	breast:
2	chr15:49572675..49575460-chr15:49576891..49580443,3	K562	blood:
3	chr15:49572227..49573901-chr15:49576450..49578887,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1023683	1.00[ASN][1000 genomes]
rs10519226	1.00[ASN][1000 genomes]
rs1055254	0.81[EUR][1000 genomes]
rs11630318	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632038	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632211	1.00[ASN][1000 genomes]
rs11632303	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632575	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633282	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634636	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635005	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635308	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635354	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635455	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635814	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638314	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638515	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11638606	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639423	1.00[ASN][1000 genomes]
rs12913966	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17394420	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17394970	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396119	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396536	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396612	0.80[EUR][1000 genomes]
rs17396747	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400427	1.00[ASN][1000 genomes]
rs17400706	0.88[EUR][1000 genomes]
rs17400916	1.00[ASN][1000 genomes]
rs17473148	1.00[ASN][1000 genomes]
rs17473568	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17475228	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17476361	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476940	0.81[EUR][1000 genomes]
rs17477722	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17478618	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479003	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078024	0.81[EUR][1000 genomes]
rs28393768	1.00[ASN][1000 genomes]
rs28408092	1.00[ASN][1000 genomes]
rs28409376	1.00[ASN][1000 genomes]
rs28430272	1.00[ASN][1000 genomes]
rs28484276	1.00[ASN][1000 genomes]
rs28669217	1.00[ASN][1000 genomes]
rs3088333	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34606419	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35692325	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57252806	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57749497	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57785991	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59112977	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59356430	0.81[EUR][1000 genomes]
rs60594237	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61259878	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61442055	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162633	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165168	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167474	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168633	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7177624	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390343	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390360	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390362	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390384	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390392	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392236	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392249	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392256	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392277	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392288	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394324	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394331	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73394333	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394355	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394357	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73394359	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396206	0.81[EUR][1000 genomes]
rs73396235	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396238	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398223	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398243	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398272	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398276	0.91[EUR][1000 genomes]
rs73398284	1.00[ASN][1000 genomes]
rs73408143	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027094	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029506	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8030457	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033311	0.81[EUR][1000 genomes]
rs8040716	1.00[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	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10519221	FGF7	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
2	chr15:49541600-49595800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:49557200-49611800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:49557800-49607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:49558000-49624400	Weak transcription	Esophagus	oesophagus
6	chr15:49558200-49611800	Weak transcription	Colonic Mucosa	Colon
7	chr15:49559200-49581400	Weak transcription	Spleen	Spleen
8	chr15:49561000-49600800	Weak transcription	Pancreas	Pancrea
9	chr15:49562000-49595800	Weak transcription	HepG2	liver
10	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:49563600-49611000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:49563800-49583200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:49564000-49580400	Weak transcription	Brain Substantia Nigra	brain
14	chr15:49564000-49580600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:49564000-49586200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:49564000-49593600	Weak transcription	HMEC	breast
17	chr15:49564200-49593600	Weak transcription	Lung	lung
18	chr15:49565400-49583600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:49565400-49602000	Weak transcription	Fetal Heart	heart
20	chr15:49565600-49583200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:49565800-49585200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:49566000-49585200	Weak transcription	GM12878-XiMat	blood
23	chr15:49566000-49586200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:49566200-49611800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:49566400-49580400	Weak transcription	Brain Hippocampus Middle	brain
26	chr15:49566400-49595600	Weak transcription	Gastric	stomach
27	chr15:49566600-49623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr15:49569000-49580800	Weak transcription	Brain Angular Gyrus	brain
29	chr15:49571000-49578600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:49572000-49583600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:49572000-49595800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:49572800-49600800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:49573400-49582800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:49573600-49579800	Strong transcription	Primary T cells from cord blood	blood
35	chr15:49573600-49613000	Weak transcription	Brain Germinal Matrix	brain
36	chr15:49573800-49578600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:49573800-49588400	Weak transcription	Fetal Kidney	kidney
38	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:49574000-49580400	Weak transcription	Fetal Brain Male	brain
40	chr15:49574000-49588400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:49574200-49578600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:49574200-49578600	Strong transcription	Dnd41	blood
43	chr15:49574200-49579600	Strong transcription	Liver	Liver
44	chr15:49574200-49580400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:49574200-49589000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr15:49574600-49588800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:49574800-49579200	Weak transcription	NHEK	skin
48	chr15:49574800-49579800	Strong transcription	K562	blood
49	chr15:49575200-49578600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr15:49575200-49578800	Strong transcription	Primary B cells from cord blood	blood

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