Variant report

Variant	rs2940747
Chromosome Location	chr15:49506241-49506242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11070686	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11636671	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12440534	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1904317	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2243899	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2246995	0.91[EUR][1000 genomes]
rs2413936	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2413939	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2413942	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2580924	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3098614	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3105865	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3105867	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4775803	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs485182	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs520949	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs532209	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs568994	0.90[EUR][1000 genomes]
rs586758	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs641077	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6493364	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8032650	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8041781	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8041823	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9920772	0.82[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
rs2940747	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463200-49508200	Weak transcription	Ovary	ovary
2	chr15:49463600-49517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:49463600-49527800	Weak transcription	HSMM	muscle
4	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
5	chr15:49465400-49508200	Weak transcription	Hela-S3	cervix
6	chr15:49480000-49510600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:49484200-49519400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:49487000-49510600	Weak transcription	Thymus	Thymus
9	chr15:49487200-49531200	Weak transcription	HMEC	breast
10	chr15:49489200-49508000	Weak transcription	Gastric	stomach
11	chr15:49489400-49508200	Weak transcription	Pancreas	Pancrea
12	chr15:49490800-49508400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:49491400-49510600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:49492000-49517600	Weak transcription	NHLF	lung
15	chr15:49492000-49520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:49492000-49527800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:49492000-49530200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:49492000-49539400	Weak transcription	Small Intestine	intestine
19	chr15:49492200-49512800	Weak transcription	NHDF-Ad	bronchial
20	chr15:49492800-49514600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:49493000-49520000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:49494000-49518600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:49495000-49509400	Weak transcription	K562	blood
24	chr15:49495000-49510600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:49495000-49515600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:49495000-49515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr15:49495000-49518000	Weak transcription	Placenta	Placenta
28	chr15:49495200-49520200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:49495400-49510400	Weak transcription	Osteobl	bone
30	chr15:49496000-49512400	Weak transcription	HUVEC	blood vessel
31	chr15:49496200-49510600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:49496400-49508200	Weak transcription	Left Ventricle	heart
33	chr15:49499200-49509000	Weak transcription	Dnd41	blood
34	chr15:49500600-49508400	Weak transcription	Stomach Mucosa	stomach
35	chr15:49501000-49508200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:49501600-49508000	Weak transcription	Fetal Heart	heart
37	chr15:49502200-49508200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:49502200-49510800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:49502400-49508200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:49503200-49511000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:49503400-49510600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:49503400-49511000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:49503600-49524000	Weak transcription	HepG2	liver
44	chr15:49503800-49508200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr15:49503800-49510800	Weak transcription	Liver	Liver
46	chr15:49504000-49508000	Weak transcription	Esophagus	oesophagus
47	chr15:49504000-49508400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr15:49504000-49509200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:49504000-49510600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:49504000-49511000	Weak transcription	Aorta	Aorta

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