Variant report

Variant	rs10519230
Chromosome Location	chr15:49748365-49748366
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10047970	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs10083602	0.84[EUR][1000 genomes]
rs10152787	0.80[EUR][1000 genomes]
rs10162802	0.80[EUR][1000 genomes]
rs10467920	0.80[EUR][1000 genomes]
rs1057636	0.80[EUR][1000 genomes]
rs1057638	0.83[EUR][1000 genomes]
rs11070692	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs11070693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070694	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11070696	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs11630629	0.89[CEU][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11631040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631687	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11631904	0.80[EUR][1000 genomes]
rs11632674	0.86[CEU][hapmap]
rs11634751	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs11636378	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs11636671	0.86[ASN][1000 genomes]
rs11636795	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11638378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs12185128	0.80[EUR][1000 genomes]
rs12437460	0.83[EUR][1000 genomes]
rs12437899	0.80[EUR][1000 genomes]
rs12438444	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12438856	0.84[EUR][1000 genomes]
rs12439479	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440099	0.80[EUR][1000 genomes]
rs12440323	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12441004	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12441304	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs12442143	0.84[EUR][1000 genomes]
rs12900001	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12913745	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1429556	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs1532955	0.86[CEU][hapmap]
rs1588130	0.86[CEU][hapmap]
rs1588131	0.80[EUR][1000 genomes]
rs1588132	0.80[EUR][1000 genomes]
rs1605481	0.86[CEU][hapmap]
rs16962243	0.82[CEU][hapmap]
rs16962486	0.94[AFR][1000 genomes]
rs16962490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962528	0.84[EUR][1000 genomes]
rs16973952	0.84[EUR][1000 genomes]
rs17401417	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1848289	0.80[EUR][1000 genomes]
rs1874612	0.80[EUR][1000 genomes]
rs1874615	0.86[CEU][hapmap]
rs1904317	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1911614	0.86[CEU][hapmap]
rs2413942	0.90[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2413946	0.84[EUR][1000 genomes]
rs2413953	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2413954	0.86[CEU][hapmap]
rs2413957	0.82[EUR][1000 genomes]
rs2413959	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs28460471	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2899433	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs4303431	0.86[CEU][hapmap]
rs4316697	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs4321137	0.83[EUR][1000 genomes]
rs4350524	0.86[CEU][hapmap]
rs4614670	0.84[EUR][1000 genomes]
rs4775811	0.83[EUR][1000 genomes]
rs4775814	0.86[CEU][hapmap]
rs4775815	0.86[CEU][hapmap]
rs56094557	0.80[EUR][1000 genomes]
rs57186766	0.83[EUR][1000 genomes]
rs57980364	0.80[EUR][1000 genomes]
rs57997677	0.80[EUR][1000 genomes]
rs58284238	0.83[EUR][1000 genomes]
rs58410445	0.84[EUR][1000 genomes]
rs60728602	0.80[EUR][1000 genomes]
rs62009983	0.80[EUR][1000 genomes]
rs6493364	0.91[CEU][hapmap];0.96[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6493369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493371	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6493376	0.86[CEU][hapmap]
rs67428220	0.80[EUR][1000 genomes]
rs67916122	0.80[EUR][1000 genomes]
rs7162351	0.80[EUR][1000 genomes]
rs7162792	0.80[EUR][1000 genomes]
rs7166049	0.84[EUR][1000 genomes]
rs7166202	0.86[CEU][hapmap]
rs7166498	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs7167041	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs7167429	0.86[CEU][hapmap]
rs7167883	0.80[EUR][1000 genomes]
rs7168031	0.80[EUR][1000 genomes]
rs7170426	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs7176350	0.80[EUR][1000 genomes]
rs7178143	0.86[CEU][hapmap]
rs7178194	0.80[EUR][1000 genomes]
rs7178468	0.86[CEU][hapmap]
rs7183313	0.80[EUR][1000 genomes]
rs733097	0.86[CEU][hapmap]
rs8026236	0.84[EUR][1000 genomes]
rs8029561	0.80[EUR][1000 genomes]
rs8031892	0.85[AFR][1000 genomes]
rs8032650	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs8034202	0.80[EUR][1000 genomes]
rs8035468	0.86[CEU][hapmap]
rs8036139	0.80[EUR][1000 genomes]
rs8039062	0.83[EUR][1000 genomes]
rs8041781	0.91[CEU][hapmap];0.96[CHB][hapmap]
rs9302148	0.82[EUR][1000 genomes]
rs965134	0.86[CEU][hapmap]
rs9920772	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9972329	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs9972429	0.84[EUR][1000 genomes]
rs9972565	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv526246	chr15:49738233-49749735	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10519230	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49732000-49750200	Weak transcription	HSMM	muscle
2	chr15:49737000-49751200	Weak transcription	Ovary	ovary
3	chr15:49742000-49752000	Weak transcription	Adipose Nuclei	Adipose
4	chr15:49742800-49750400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:49743200-49748400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:49747200-49749000	Enhancers	Colon Smooth Muscle	Colon
7	chr15:49747200-49749200	Enhancers	Rectal Smooth Muscle	rectum
8	chr15:49747200-49751400	Enhancers	NHDF-Ad	bronchial
9	chr15:49747200-49752600	Enhancers	Osteobl	bone
10	chr15:49747400-49748400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:49747400-49753000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:49747600-49751400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:49748000-49749000	Enhancers	Fetal Heart	heart
14	chr15:49748000-49749200	Enhancers	Fetal Lung	lung
15	chr15:49748000-49750400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:49748200-49749200	Enhancers	NHLF	lung
17	chr15:49748200-49749600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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