Variant report

Variant	rs12440709
Chromosome Location	chr15:49395250-49395251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GALK2-1	chr15:49395139-49395461	ENSG00000259656.1

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10431775	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1048975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10775139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070682	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070683	0.81[AMR][1000 genomes]
rs11629547	0.80[ASN][1000 genomes]
rs11633810	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs11637991	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11638215	0.81[CEU][hapmap]
rs11855740	0.82[CEU][hapmap]
rs11858114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs12148348	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12438777	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12442679	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12898691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902875	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904344	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs16962057	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2086256	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2127241	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2127242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2247517	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs2413928	0.84[EUR][1000 genomes]
rs2413931	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2457228	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2580923	0.80[ASN][1000 genomes]
rs2580926	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2663088	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2663089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2663090	0.86[ASN][1000 genomes]
rs28676698	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28724568	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2899427	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2899430	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs2899431	0.90[JPT][hapmap]
rs2940745	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3098613	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3098615	0.80[ASN][1000 genomes]
rs3098619	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3098620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs3098621	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs3105858	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs3105861	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3105863	0.80[ASN][1000 genomes]
rs3105864	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3105866	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs34854443	0.80[ASN][1000 genomes]
rs3907313	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs4284578	0.82[CEU][hapmap]
rs4536401	0.82[CEU][hapmap]
rs4774537	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs4775795	0.82[CEU][hapmap]
rs481466	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs489813	0.89[CHB][hapmap]
rs490621	0.86[ASN][1000 genomes]
rs563533	0.80[ASN][1000 genomes]
rs568726	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs600863	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs603868	0.82[ASN][1000 genomes]
rs604765	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs612803	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs62013266	0.93[ASN][1000 genomes]
rs626295	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs626855	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs647118	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs6493346	0.81[CEU][hapmap]
rs6493356	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs6493357	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs679957	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs685172	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7162602	0.83[EUR][1000 genomes]
rs7165264	0.82[CEU][hapmap]
rs7166847	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs7167402	0.81[CEU][hapmap]
rs7179301	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8029914	0.81[CEU][hapmap]
rs877007	0.82[CEU][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12440709	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49376400-49397800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:49376600-49397600	Weak transcription	NHLF	lung
3	chr15:49378800-49396800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:49381400-49397400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:49381400-49402400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:49381600-49398000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:49381800-49395600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:49382600-49402400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:49385600-49403200	Weak transcription	Placenta	Placenta
10	chr15:49386400-49403400	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:49386400-49404200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:49386800-49402600	Weak transcription	Gastric	stomach
13	chr15:49387000-49397400	Weak transcription	Primary T cells from cord blood	blood
14	chr15:49387200-49397600	Weak transcription	HSMMtube	muscle
15	chr15:49387200-49397800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:49387200-49402400	Weak transcription	Spleen	Spleen
17	chr15:49387200-49403000	Weak transcription	Dnd41	blood
18	chr15:49387400-49404200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:49388800-49395800	Weak transcription	Liver	Liver
20	chr15:49388800-49396800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:49388800-49396800	Weak transcription	Fetal Intestine Large	intestine
22	chr15:49388800-49397400	Weak transcription	K562	blood
23	chr15:49388800-49402400	Weak transcription	Fetal Intestine Small	intestine
24	chr15:49388800-49402400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:49388800-49402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:49388800-49402600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:49388800-49402600	Weak transcription	Left Ventricle	heart
28	chr15:49388800-49402600	Weak transcription	Ovary	ovary
29	chr15:49388800-49402600	Weak transcription	Pancreas	Pancrea
30	chr15:49388800-49402600	Weak transcription	Thymus	Thymus
31	chr15:49388800-49402800	Weak transcription	Lung	lung
32	chr15:49388800-49404400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:49388800-49404600	Weak transcription	Hela-S3	cervix
34	chr15:49388800-49418800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:49388800-49434800	Weak transcription	Small Intestine	intestine
36	chr15:49389600-49396000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:49389600-49404400	Weak transcription	HepG2	liver
38	chr15:49390400-49403000	Weak transcription	Aorta	Aorta
39	chr15:49390800-49403000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:49391200-49398000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:49391200-49402400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr15:49391400-49397400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr15:49391400-49402400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:49391400-49402600	Weak transcription	Fetal Muscle Leg	muscle
45	chr15:49391400-49404200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:49391600-49397800	Weak transcription	NHDF-Ad	bronchial
47	chr15:49391600-49402400	Weak transcription	Esophagus	oesophagus
48	chr15:49391600-49402600	Weak transcription	Fetal Stomach	stomach
49	chr15:49391800-49397600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:49391800-49403400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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