Variant report

Variant	rs9806748
Chromosome Location	chr15:49632116-49632117
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10467992	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10851475	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11632063	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11858114	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1812926	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1904314	0.83[EUR][1000 genomes]
rs2086256	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2127241	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2127242	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2127244	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2169932	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2219812	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2413937	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2580923	0.80[EUR][1000 genomes]
rs2580926	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2663088	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28479967	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28728368	0.84[EUR][1000 genomes]
rs2899430	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2919148	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3098615	0.83[EUR][1000 genomes]
rs3098620	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3105861	0.80[EUR][1000 genomes]
rs3105863	0.81[EUR][1000 genomes]
rs4775804	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4775805	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4775807	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4775809	0.85[EUR][1000 genomes]
rs500122	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493361	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6493363	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7167555	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7176455	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs735495	0.84[EUR][1000 genomes]
rs754165	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs754166	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8025952	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8034661	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8040075	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9806748	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs9806748	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49599200-49636800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:49612200-49639000	Weak transcription	NHEK	skin
3	chr15:49612600-49639400	Weak transcription	Right Ventricle	heart
4	chr15:49612800-49638000	Weak transcription	Brain Angular Gyrus	brain
5	chr15:49613000-49633200	Weak transcription	Gastric	stomach
6	chr15:49613200-49633200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr15:49613600-49633800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:49613600-49637200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:49613600-49643000	Weak transcription	Pancreas	Pancrea
10	chr15:49613800-49632600	Weak transcription	Fetal Thymus	thymus
11	chr15:49613800-49639800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:49614200-49637200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr15:49614200-49640200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:49614200-49640200	Weak transcription	Small Intestine	intestine
15	chr15:49614400-49633400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:49614400-49634000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:49614800-49639000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:49615800-49633600	Weak transcription	Placenta	Placenta
19	chr15:49615800-49636600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:49616000-49641400	Weak transcription	Fetal Lung	lung
21	chr15:49617800-49633000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:49622600-49632200	Weak transcription	Thymus	Thymus
23	chr15:49622600-49642600	Weak transcription	HSMM	muscle
24	chr15:49623000-49633800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:49623000-49640200	Weak transcription	Primary T cells from cord blood	blood
26	chr15:49623200-49646000	Weak transcription	Left Ventricle	heart
27	chr15:49623400-49632600	Weak transcription	Dnd41	blood
28	chr15:49623400-49635800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr15:49623400-49636800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:49623400-49638200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:49623400-49638400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:49623400-49639600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr15:49623400-49639800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr15:49623400-49640000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:49623400-49647600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:49623800-49640200	Weak transcription	Liver	Liver
37	chr15:49628400-49633800	Weak transcription	Spleen	Spleen
38	chr15:49628600-49640800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:49629400-49639000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:49631000-49636200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:49631400-49632600	ZNF genes & repeats	Fetal Stomach	stomach
42	chr15:49631600-49632200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:49631600-49632200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:49631600-49632400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr15:49631600-49632400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:49631600-49632400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:49631600-49632400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
48	chr15:49631600-49632400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:49631600-49632400	Strong transcription	Lung	lung
50	chr15:49631600-49632600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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