Variant report

Variant	rs12439479
Chromosome Location	chr15:49734843-49734844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10047970	0.81[EUR][1000 genomes]
rs10083602	0.83[EUR][1000 genomes]
rs10519230	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057638	0.81[EUR][1000 genomes]
rs11070692	0.86[AFR][1000 genomes]
rs11070693	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070694	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11070696	0.80[EUR][1000 genomes]
rs11630629	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11631040	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631687	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11636671	0.86[ASN][1000 genomes]
rs11636795	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11638378	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437460	0.81[EUR][1000 genomes]
rs12438444	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12438856	0.83[EUR][1000 genomes]
rs12440323	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12441004	0.81[AMR][1000 genomes]
rs12442143	0.83[EUR][1000 genomes]
rs12900001	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12913745	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1429556	0.87[AFR][1000 genomes]
rs16962486	0.95[AFR][1000 genomes]
rs16962490	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962528	0.83[EUR][1000 genomes]
rs16973952	0.83[EUR][1000 genomes]
rs17401417	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2413942	0.85[ASN][1000 genomes]
rs2413946	0.83[EUR][1000 genomes]
rs2413957	0.81[EUR][1000 genomes]
rs2413959	0.80[EUR][1000 genomes]
rs28460471	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2899433	0.82[EUR][1000 genomes]
rs4316697	0.89[AFR][1000 genomes]
rs4321137	0.81[EUR][1000 genomes]
rs4614670	0.83[EUR][1000 genomes]
rs4775811	0.81[EUR][1000 genomes]
rs57186766	0.81[EUR][1000 genomes]
rs58284238	0.81[EUR][1000 genomes]
rs58410445	0.83[EUR][1000 genomes]
rs6493364	0.86[ASN][1000 genomes]
rs6493369	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493371	0.83[EUR][1000 genomes]
rs7166049	0.83[EUR][1000 genomes]
rs7166498	0.83[EUR][1000 genomes]
rs7167041	0.83[EUR][1000 genomes]
rs7170426	0.83[EUR][1000 genomes]
rs8026236	0.83[EUR][1000 genomes]
rs8031892	0.86[AFR][1000 genomes]
rs8039062	0.81[EUR][1000 genomes]
rs9302148	0.80[EUR][1000 genomes]
rs9920772	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9972329	0.83[EUR][1000 genomes]
rs9972429	0.83[EUR][1000 genomes]
rs9972565	0.83[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	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
2	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
3	nsv9263	chr15:49734435-49809465	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12439479	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49716400-49737200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:49721000-49736200	Weak transcription	Right Ventricle	heart
3	chr15:49730400-49744600	Weak transcription	NHLF	lung
4	chr15:49732000-49736600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:49732000-49750200	Weak transcription	HSMM	muscle
6	chr15:49732200-49736200	Weak transcription	Ovary	ovary
7	chr15:49732200-49736200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:49732400-49736800	Weak transcription	Fetal Stomach	stomach
9	chr15:49732400-49738200	Weak transcription	NHDF-Ad	bronchial
10	chr15:49732800-49741000	Weak transcription	Fetal Heart	heart
11	chr15:49733200-49735200	Enhancers	Colon Smooth Muscle	Colon
12	chr15:49733200-49741800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:49733600-49735200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:49733800-49736200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:49734400-49735200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr15:49734400-49736400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:49734600-49735000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr15:49734600-49735200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr15:49734600-49735200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr15:49734600-49735400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:49734800-49735200	Enhancers	Rectal Smooth Muscle	rectum
22	chr15:49734800-49736600	Weak transcription	Osteobl	bone

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