Variant report

Variant	rs12902875
Chromosome Location	chr15:49408139-49408140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10431775	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1048975	0.90[ASN][1000 genomes]
rs10775139	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070682	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11629547	0.83[ASN][1000 genomes]
rs11632063	0.81[ASN][1000 genomes]
rs11637991	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11858114	0.81[ASN][1000 genomes]
rs12148348	0.82[EUR][1000 genomes]
rs12440709	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442679	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12898691	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962057	0.82[EUR][1000 genomes]
rs2413928	0.81[EUR][1000 genomes]
rs2413931	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2413935	0.85[ASN][1000 genomes]
rs2413937	0.81[ASN][1000 genomes]
rs2457228	0.81[ASN][1000 genomes]
rs2580923	0.83[ASN][1000 genomes]
rs2663089	0.83[ASN][1000 genomes]
rs2663090	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28479967	0.81[ASN][1000 genomes]
rs28539950	0.81[ASN][1000 genomes]
rs28676698	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28724568	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28728368	0.81[ASN][1000 genomes]
rs28731311	0.81[ASN][1000 genomes]
rs2899427	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2899430	0.81[ASN][1000 genomes]
rs2919148	0.81[ASN][1000 genomes]
rs2940745	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3098615	0.83[ASN][1000 genomes]
rs3098620	0.81[ASN][1000 genomes]
rs3105861	0.83[ASN][1000 genomes]
rs3105863	0.83[ASN][1000 genomes]
rs34854443	0.83[ASN][1000 genomes]
rs490621	0.88[ASN][1000 genomes]
rs491277	0.81[ASN][1000 genomes]
rs500122	0.81[ASN][1000 genomes]
rs55736202	0.81[ASN][1000 genomes]
rs563533	0.83[ASN][1000 genomes]
rs568726	0.81[ASN][1000 genomes]
rs600863	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs603868	0.85[ASN][1000 genomes]
rs62013266	0.90[ASN][1000 genomes]
rs626855	0.81[ASN][1000 genomes]
rs671945	0.82[ASN][1000 genomes]
rs679957	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs685172	0.81[ASN][1000 genomes]
rs7162602	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7179301	0.82[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12902875	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49388800-49418800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:49388800-49434800	Weak transcription	Small Intestine	intestine
3	chr15:49393600-49413200	Weak transcription	HMEC	breast
4	chr15:49395400-49419000	Weak transcription	Fetal Kidney	kidney
5	chr15:49395600-49426400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:49396000-49419600	Weak transcription	NHEK	skin
7	chr15:49396400-49418800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:49398600-49427600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:49399200-49414600	Weak transcription	HUVEC	blood vessel
10	chr15:49403000-49417200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:49403000-49434600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:49403200-49408200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:49403200-49413000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:49403200-49423400	Weak transcription	Psoas Muscle	Psoas
15	chr15:49403400-49419600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:49403400-49440200	Weak transcription	Pancreas	Pancrea
17	chr15:49403600-49411200	Weak transcription	Fetal Intestine Small	intestine
18	chr15:49403600-49423600	Weak transcription	Esophagus	oesophagus
19	chr15:49403600-49432200	Weak transcription	Fetal Stomach	stomach
20	chr15:49403600-49435200	Weak transcription	Aorta	Aorta
21	chr15:49403600-49435200	Weak transcription	Gastric	stomach
22	chr15:49403600-49435400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:49403800-49417400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:49403800-49419400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:49403800-49433200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:49404000-49419800	Weak transcription	NHLF	lung
27	chr15:49404400-49419800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr15:49404600-49424000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr15:49404800-49415400	Weak transcription	Hela-S3	cervix
30	chr15:49404800-49417200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:49404800-49417600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:49404800-49419000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:49404800-49419000	Weak transcription	Primary T cells from cord blood	blood
34	chr15:49404800-49419000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:49404800-49419200	Weak transcription	Brain Angular Gyrus	brain
36	chr15:49404800-49419400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr15:49404800-49419400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:49404800-49419400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:49404800-49419600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:49404800-49419600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:49404800-49419600	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:49404800-49419600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:49404800-49419600	Weak transcription	Ovary	ovary
44	chr15:49404800-49419600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:49404800-49419800	Weak transcription	Left Ventricle	heart
46	chr15:49404800-49419800	Weak transcription	Thymus	Thymus
47	chr15:49404800-49423400	Weak transcription	HepG2	liver
48	chr15:49404800-49425600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:49404800-49434600	Weak transcription	Right Ventricle	heart
50	chr15:49404800-49435000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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