Variant report

Variant	rs2413942
Chromosome Location	chr15:49645276-49645277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10467992	0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs10519230	0.90[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11070686	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070693	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11630629	0.88[CEU][hapmap]
rs11631040	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11631687	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11634751	0.80[CEU][hapmap]
rs11636378	0.85[CEU][hapmap]
rs11636671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11636795	0.90[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11638378	0.85[ASN][1000 genomes]
rs11852524	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs11858114	0.84[YRI][hapmap]
rs12439479	0.85[ASN][1000 genomes]
rs12440534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12441304	0.80[CEU][hapmap]
rs12900001	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs12913745	0.88[ASN][1000 genomes]
rs1588130	0.80[CEU][hapmap]
rs1605481	0.80[CEU][hapmap]
rs16962243	0.82[JPT][hapmap]
rs16962490	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1904317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2127241	0.81[YRI][hapmap]
rs2243899	0.84[AFR][1000 genomes]
rs2246995	0.84[AFR][1000 genomes]
rs2413936	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2413939	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413954	0.84[CEU][hapmap]
rs2413959	0.80[CEU][hapmap]
rs2580924	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2663088	0.81[YRI][hapmap]
rs2940747	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3098614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3105861	0.81[YRI][hapmap]
rs3105865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3105867	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4468544	0.80[AFR][1000 genomes]
rs4775803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs485182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs520949	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs532209	0.87[AFR][1000 genomes]
rs568994	0.84[AFR][1000 genomes]
rs586758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs641077	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6493361	0.81[YRI][hapmap]
rs6493363	0.84[YRI][hapmap]
rs6493364	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493369	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs7497114	0.80[AFR][1000 genomes]
rs754165	0.81[YRI][hapmap]
rs8032650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8035468	0.80[CEU][hapmap]
rs8040075	0.81[YRI][hapmap]
rs8041781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8041823	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs965134	0.80[CEU][hapmap]
rs9920772	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2413942	GALK2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49623200-49646000	Weak transcription	Left Ventricle	heart
2	chr15:49623400-49647600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:49644600-49646600	Weak transcription	Aorta	Aorta
4	chr15:49645200-49645400	Enhancers	HUVEC	blood vessel

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