Variant report

Variant	rs2413939
Chromosome Location	chr15:49511379-49511380
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49509199..49512109-chr15:49514145..49516432,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11070686	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11632063	0.82[AMR][1000 genomes]
rs11636671	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11858114	0.82[AMR][1000 genomes]
rs12440534	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812926	0.82[AMR][1000 genomes]
rs1904317	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2086256	0.82[AMR][1000 genomes]
rs2127241	0.81[AMR][1000 genomes]
rs2127242	0.81[AMR][1000 genomes]
rs2127244	0.82[AMR][1000 genomes]
rs2169932	0.81[AMR][1000 genomes]
rs2243899	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2246995	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2413936	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413937	0.82[AMR][1000 genomes]
rs2413942	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2580924	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2580926	0.82[AMR][1000 genomes]
rs2663088	0.82[AMR][1000 genomes]
rs2899430	0.81[AMR][1000 genomes]
rs2919148	0.81[AMR][1000 genomes]
rs2940747	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3098614	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3098620	0.82[AMR][1000 genomes]
rs3105865	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3105867	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4775803	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775804	0.81[AMR][1000 genomes]
rs4775805	0.82[AMR][1000 genomes]
rs485182	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs500122	0.82[AMR][1000 genomes]
rs520949	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs532209	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568994	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs586758	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs641077	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493364	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7167555	0.82[AMR][1000 genomes]
rs7176455	0.82[AMR][1000 genomes]
rs754165	0.81[AMR][1000 genomes]
rs754166	0.81[AMR][1000 genomes]
rs8032650	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8041781	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8041823	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920772	0.84[AMR][1000 genomes];0.80[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2413939	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463600-49517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:49463600-49527800	Weak transcription	HSMM	muscle
3	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
4	chr15:49484200-49519400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:49487200-49531200	Weak transcription	HMEC	breast
6	chr15:49492000-49517600	Weak transcription	NHLF	lung
7	chr15:49492000-49520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:49492000-49527800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:49492000-49530200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:49492000-49539400	Weak transcription	Small Intestine	intestine
11	chr15:49492200-49512800	Weak transcription	NHDF-Ad	bronchial
12	chr15:49492800-49514600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:49493000-49520000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:49494000-49518600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:49495000-49515600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:49495000-49515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr15:49495000-49518000	Weak transcription	Placenta	Placenta
18	chr15:49495200-49520200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:49496000-49512400	Weak transcription	HUVEC	blood vessel
20	chr15:49503600-49524000	Weak transcription	HepG2	liver
21	chr15:49504000-49512400	Weak transcription	Fetal Brain Female	brain
22	chr15:49504200-49513000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:49504200-49513800	Weak transcription	Fetal Lung	lung
24	chr15:49504200-49520200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:49504200-49530800	Weak transcription	Fetal Thymus	thymus
26	chr15:49506400-49513600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:49507200-49517400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:49507400-49515600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:49508400-49511400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr15:49508400-49512600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr15:49508600-49515600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:49508600-49517400	Weak transcription	Right Ventricle	heart
33	chr15:49508800-49515000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr15:49508800-49515800	Weak transcription	Psoas Muscle	Psoas
35	chr15:49508800-49517400	Weak transcription	Esophagus	oesophagus
36	chr15:49508800-49517600	Weak transcription	Spleen	Spleen
37	chr15:49508800-49521600	Weak transcription	Hela-S3	cervix
38	chr15:49508800-49535800	Weak transcription	A549	lung
39	chr15:49509000-49512800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:49509000-49513600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:49509000-49517400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr15:49509000-49517400	Weak transcription	Pancreas	Pancrea
43	chr15:49509000-49517400	Weak transcription	Right Atrium	heart
44	chr15:49509200-49511600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:49509200-49517400	Weak transcription	Primary B cells from cord blood	blood
46	chr15:49509200-49517400	Weak transcription	Gastric	stomach
47	chr15:49509200-49517800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:49509400-49511800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:49509400-49513000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:49509400-49517200	Weak transcription	Fetal Heart	heart

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