Variant report

Variant	rs4775804
Chromosome Location	chr15:49547910-49547911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10467992	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10851475	0.81[AMR][1000 genomes]
rs11629547	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11632063	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858114	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1812926	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2086256	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2127241	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2127242	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2127244	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2169932	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2219812	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2263559	0.90[ASN][1000 genomes]
rs2413935	0.84[ASN][1000 genomes]
rs2413937	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2413939	0.81[AMR][1000 genomes]
rs2457228	0.88[ASN][1000 genomes]
rs2580923	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2580926	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2663088	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2663089	0.82[ASN][1000 genomes]
rs2663090	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28437582	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28479967	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28539950	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28728368	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28731311	0.88[ASN][1000 genomes]
rs2899430	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2919148	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2940745	0.85[EUR][1000 genomes]
rs2940746	0.90[ASN][1000 genomes]
rs3098615	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3098620	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3105861	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3105863	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34854443	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775805	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775807	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs490621	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs500122	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55736202	0.88[ASN][1000 genomes]
rs563533	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs568726	0.88[ASN][1000 genomes]
rs600863	0.85[EUR][1000 genomes]
rs603868	0.84[ASN][1000 genomes]
rs626855	0.88[ASN][1000 genomes]
rs6493361	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6493363	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs671945	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs679957	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs685172	0.88[ASN][1000 genomes]
rs7167338	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167555	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7176455	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs754165	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs754166	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8025952	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034661	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8040075	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9806748	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv569342	chr15:49529302-49549943	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv569347	chr15:49534702-49549943	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv569354	chr15:49540216-49549943	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3508350	chr15:49543710-49549008	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3311210	chr15:49544060-49548858	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3508349	chr15:49544110-49548908	Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3508354	chr15:49544404-49548543	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3311209	chr15:49544434-49548137	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3508355	chr15:49544719-49547965	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3311206	chr15:49544726-49547931	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3311211	chr15:49544727-49547945	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3508351	chr15:49544733-49547936	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv3311207	chr15:49544783-49547927	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv569364	chr15:49545009-49549943	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv569365	chr15:49545009-49557933	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv569374	chr15:49545192-49549943	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv569375	chr15:49545192-49557933	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv569385	chr15:49545780-49549943	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv569390	chr15:49546263-49549943	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv569391	chr15:49546424-49549943	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4775804	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49518200-49548600	Weak transcription	Aorta	Aorta
2	chr15:49518600-49557600	Weak transcription	Esophagus	oesophagus
3	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
4	chr15:49522400-49559400	Weak transcription	Pancreas	Pancrea
5	chr15:49528000-49576000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:49529200-49550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:49533400-49548200	Weak transcription	HMEC	breast
8	chr15:49533800-49576200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:49535600-49557000	Weak transcription	Fetal Intestine Small	intestine
10	chr15:49535600-49564600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr15:49535600-49574200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:49535600-49574200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:49535800-49549200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:49535800-49563400	Weak transcription	NH-A	brain
15	chr15:49535800-49566800	Weak transcription	Left Ventricle	heart
16	chr15:49535800-49575800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:49536200-49549400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:49536200-49549800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr15:49536200-49553200	Weak transcription	Primary B cells from cord blood	blood
20	chr15:49537600-49566000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:49537800-49549000	Weak transcription	Liver	Liver
22	chr15:49538600-49550400	Weak transcription	HSMM	muscle
23	chr15:49539400-49553200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:49539600-49563000	Weak transcription	Ovary	ovary
25	chr15:49540000-49550400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr15:49540000-49550400	Weak transcription	NHDF-Ad	bronchial
27	chr15:49540000-49552200	Weak transcription	Fetal Muscle Leg	muscle
28	chr15:49540000-49566200	Weak transcription	K562	blood
29	chr15:49540000-49577600	Weak transcription	Small Intestine	intestine
30	chr15:49540200-49552200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr15:49540600-49557400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:49540800-49548400	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:49541400-49551400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:49541400-49562600	Weak transcription	Dnd41	blood
35	chr15:49541600-49548400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:49541600-49557200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:49541600-49575000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:49541600-49595800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:49541800-49548400	Weak transcription	Fetal Kidney	kidney
40	chr15:49541800-49558800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr15:49542000-49560800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr15:49542200-49548000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr15:49542200-49557200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr15:49542400-49550600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:49542800-49548600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:49542800-49560800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:49543000-49550600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:49543200-49550200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:49543200-49558000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:49543400-49548000	Weak transcription	Osteobl	bone

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