Variant report

Variant	rs10851475
Chromosome Location	chr15:49625930-49625931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10467992	0.88[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10467993	0.91[ASN][1000 genomes]
rs10851476	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs11070687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11070692	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs11632063	0.81[AMR][1000 genomes]
rs11854667	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11858114	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs12438777	0.84[CHB][hapmap]
rs12902497	0.88[ASN][1000 genomes]
rs12903238	0.88[ASN][1000 genomes]
rs12903904	0.88[ASN][1000 genomes]
rs12909779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12916840	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1429556	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs1594188	0.87[ASN][1000 genomes]
rs1812926	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1816293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1864299	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs1904313	0.87[ASN][1000 genomes]
rs1904314	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1904317	0.81[GIH][hapmap]
rs1981995	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs2043036	0.88[ASN][1000 genomes]
rs2086256	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2099141	0.87[ASN][1000 genomes]
rs2127241	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2127242	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2127244	0.81[AMR][1000 genomes]
rs2163095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2163096	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2169932	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2219812	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2247517	0.85[CHB][hapmap]
rs2413937	0.81[AMR][1000 genomes]
rs2580926	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs2663088	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs28374976	0.87[ASN][1000 genomes]
rs28687437	0.87[ASN][1000 genomes]
rs2899430	0.88[CEU][hapmap]
rs2899431	0.84[CHB][hapmap]
rs3098613	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs3098619	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs3098620	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs3098621	0.85[CHB][hapmap]
rs3105858	0.85[CHB][hapmap]
rs3105861	0.88[CEU][hapmap]
rs3105864	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs3105866	0.85[CHB][hapmap]
rs3907313	0.85[CHB][hapmap]
rs4316697	0.81[CEU][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap]
rs4421927	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4508377	0.92[ASN][1000 genomes]
rs4774537	0.85[CHB][hapmap]
rs4775804	0.81[AMR][1000 genomes]
rs4775805	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4775807	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4775809	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4775810	0.87[ASN][1000 genomes]
rs481466	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs489813	0.84[CHB][hapmap]
rs500122	0.81[AMR][1000 genomes]
rs520949	0.81[GIH][hapmap]
rs604765	0.85[CHB][hapmap]
rs612803	0.85[CHB][hapmap]
rs626295	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs647118	0.88[CEU][hapmap]
rs6493356	0.85[CHB][hapmap]
rs6493357	0.84[CHB][hapmap]
rs6493361	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs6493362	0.92[ASN][1000 genomes]
rs6493363	0.88[CEU][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs679957	0.88[CEU][hapmap]
rs7162360	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7166847	0.85[CHB][hapmap]
rs7167555	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7168201	0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs7173761	0.88[ASN][1000 genomes]
rs7176455	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7179127	0.85[CHB][hapmap]
rs7179237	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs735495	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs754165	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs754166	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8024102	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8025237	0.88[ASN][1000 genomes]
rs8025952	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8031480	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs8032650	0.81[GIH][hapmap]
rs8034112	0.88[ASN][1000 genomes]
rs8034661	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8034747	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs8034956	0.91[ASN][1000 genomes]
rs8035266	0.90[ASN][1000 genomes]
rs8039920	0.92[ASN][1000 genomes]
rs8040075	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8040134	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs8041461	0.92[ASN][1000 genomes]
rs919447	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9806208	0.92[ASN][1000 genomes]
rs9806748	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9806776	0.85[ASN][1000 genomes]
rs981612	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10851475	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:49582600-49628200	Weak transcription	Spleen	Spleen
3	chr15:49599200-49636800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:49608000-49631800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:49608600-49631800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:49612200-49631600	Weak transcription	Fetal Intestine Small	intestine
7	chr15:49612200-49639000	Weak transcription	NHEK	skin
8	chr15:49612600-49639400	Weak transcription	Right Ventricle	heart
9	chr15:49612800-49626600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:49612800-49638000	Weak transcription	Brain Angular Gyrus	brain
11	chr15:49613000-49627600	Weak transcription	HUVEC	blood vessel
12	chr15:49613000-49628200	Weak transcription	Ovary	ovary
13	chr15:49613000-49633200	Weak transcription	Gastric	stomach
14	chr15:49613200-49633200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr15:49613600-49633800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:49613600-49637200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:49613600-49643000	Weak transcription	Pancreas	Pancrea
18	chr15:49613800-49632600	Weak transcription	Fetal Thymus	thymus
19	chr15:49613800-49639800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:49614200-49631600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:49614200-49631600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:49614200-49631800	Weak transcription	Aorta	Aorta
23	chr15:49614200-49632000	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:49614200-49637200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr15:49614200-49640200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:49614200-49640200	Weak transcription	Small Intestine	intestine
27	chr15:49614400-49633400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:49614400-49634000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:49614800-49628800	Weak transcription	Osteobl	bone
30	chr15:49614800-49631800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:49614800-49639000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:49615600-49628400	Weak transcription	Adipose Nuclei	Adipose
33	chr15:49615800-49626600	Weak transcription	Fetal Stomach	stomach
34	chr15:49615800-49633600	Weak transcription	Placenta	Placenta
35	chr15:49615800-49636600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:49616000-49641400	Weak transcription	Fetal Lung	lung
37	chr15:49616600-49632000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:49617800-49633000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:49618000-49626800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:49622400-49631600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr15:49622600-49631600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:49622600-49631600	Weak transcription	Fetal Intestine Large	intestine
43	chr15:49622600-49631800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:49622600-49632200	Weak transcription	Thymus	Thymus
45	chr15:49622600-49642600	Weak transcription	HSMM	muscle
46	chr15:49622800-49631800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:49623000-49628000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:49623000-49628600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:49623000-49631800	Weak transcription	Primary B cells from cord blood	blood
50	chr15:49623000-49633800	Weak transcription	Rectal Mucosa Donor 29	rectum

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