Variant report

Variant	rs6493369
Chromosome Location	chr15:49706467-49706468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10047970	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs10083602	0.81[EUR][1000 genomes]
rs10519230	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]
rs1057638	0.80[EUR][1000 genomes]
rs11070693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070694	0.81[EUR][1000 genomes]
rs11070696	0.81[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs11630629	0.89[CEU][hapmap]
rs11631040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631687	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632674	0.86[CEU][hapmap]
rs11634751	0.86[CEU][hapmap]
rs11636378	0.81[CEU][hapmap]
rs11636671	0.87[ASN][1000 genomes]
rs11636795	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638378	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11852524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs12437460	0.80[EUR][1000 genomes]
rs12438444	0.80[EUR][1000 genomes]
rs12438856	0.81[EUR][1000 genomes]
rs12439479	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12440323	0.86[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12440534	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs12441304	0.86[CEU][hapmap]
rs12442143	0.81[EUR][1000 genomes]
rs12442701	0.80[EUR][1000 genomes]
rs12900001	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913745	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1532955	0.86[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs1588130	0.86[CEU][hapmap]
rs1605481	0.86[CEU][hapmap]
rs16962243	0.82[CEU][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap]
rs16962490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16962528	0.81[EUR][1000 genomes]
rs16973952	0.81[EUR][1000 genomes]
rs17401417	0.81[EUR][1000 genomes]
rs1874615	0.86[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs1904317	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs1911614	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs2413942	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2413946	0.81[EUR][1000 genomes]
rs2413953	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2413954	0.86[CEU][hapmap]
rs2413959	0.86[CEU][hapmap]
rs28460471	0.80[EUR][1000 genomes]
rs2899433	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4303431	0.86[CEU][hapmap]
rs4316697	0.92[GIH][hapmap]
rs4321137	0.80[EUR][1000 genomes]
rs4350524	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs4614670	0.81[EUR][1000 genomes]
rs4775803	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4775811	0.80[EUR][1000 genomes]
rs4775814	0.86[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs4775815	0.86[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs520949	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs57186766	0.80[EUR][1000 genomes]
rs58284238	0.80[EUR][1000 genomes]
rs58410445	0.81[EUR][1000 genomes]
rs586758	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap]
rs6493364	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6493371	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6493376	0.86[CEU][hapmap]
rs7162800	0.83[MEX][hapmap]
rs7166049	0.81[EUR][1000 genomes]
rs7166202	0.86[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs7166498	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7167041	0.86[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7167429	0.86[CEU][hapmap]
rs7170426	0.86[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7178143	0.86[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs7178468	0.86[CEU][hapmap]
rs733097	0.86[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs8026236	0.81[EUR][1000 genomes]
rs8032650	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap]
rs8035468	0.86[CEU][hapmap]
rs8039062	0.80[EUR][1000 genomes]
rs8041781	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs965134	0.86[CEU][hapmap]
rs9920772	0.88[ASN][1000 genomes]
rs9972329	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9972429	0.81[EUR][1000 genomes]
rs9972565	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6493369	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs6493369	DTWD1	cis	cerebellum	SCAN
rs6493369	SHC4	cis	lymphoblastoid	seeQTL
rs6493369	CATSPER2P1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49703000-49709600	Weak transcription	Fetal Lung	lung
2	chr15:49703400-49707400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:49703600-49707200	Weak transcription	NHDF-Ad	bronchial
4	chr15:49705800-49707400	Enhancers	Primary neutrophils fromperipheralblood	blood

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