Variant report

Variant	rs12916154
Chromosome Location	chr15:50233606-50233607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10519246	1.00[ASN][1000 genomes]
rs10519248	1.00[ASN][1000 genomes]
rs10519250	0.91[GIH][hapmap]
rs12101700	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12101710	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12101847	0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12593937	0.85[GIH][hapmap]
rs12899404	1.00[ASN][1000 genomes]
rs12904852	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905192	1.00[ASN][1000 genomes]
rs12905409	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905434	0.91[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs12907398	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329614	1.00[ASN][1000 genomes]
rs16963032	1.00[ASN][1000 genomes]
rs16963056	1.00[ASN][1000 genomes]
rs16963064	1.00[ASN][1000 genomes]
rs16963067	1.00[ASN][1000 genomes]
rs16963076	1.00[ASN][1000 genomes]
rs16963083	1.00[ASN][1000 genomes]
rs2067885	0.88[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2413977	0.88[GIH][hapmap]
rs2413979	1.00[ASN][1000 genomes]
rs2413983	0.82[ASW][hapmap];0.88[CEU][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2413992	0.85[GIH][hapmap]
rs28406046	1.00[ASN][1000 genomes]
rs28412330	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28416417	1.00[ASN][1000 genomes]
rs28437808	1.00[ASN][1000 genomes]
rs28502034	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28555213	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28627943	1.00[ASN][1000 genomes]
rs28640908	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28649135	1.00[ASN][1000 genomes]
rs28669725	1.00[ASN][1000 genomes]
rs28687946	1.00[ASN][1000 genomes]
rs28698041	1.00[ASN][1000 genomes]
rs28699236	1.00[ASN][1000 genomes]
rs28756960	1.00[ASN][1000 genomes]
rs28809909	1.00[ASN][1000 genomes]
rs28823045	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28836239	1.00[ASN][1000 genomes]
rs28837213	1.00[ASN][1000 genomes]
rs28844958	1.00[ASN][1000 genomes]
rs28856727	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28861197	1.00[ASN][1000 genomes]
rs28862395	1.00[ASN][1000 genomes]
rs28866824	1.00[ASN][1000 genomes]
rs28868411	1.00[ASN][1000 genomes]
rs28874321	1.00[ASN][1000 genomes]
rs28877101	1.00[ASN][1000 genomes]
rs34707020	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4349086	0.88[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs4407015	1.00[ASN][1000 genomes]
rs4426299	1.00[ASN][1000 genomes]
rs4433752	0.88[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs4491453	1.00[ASN][1000 genomes]
rs7175764	0.88[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs7183166	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7350791	1.00[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7350796	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74012838	1.00[ASN][1000 genomes]
rs74012843	1.00[ASN][1000 genomes]
rs7496373	1.00[ASN][1000 genomes]
rs8027073	0.85[GIH][hapmap]
rs8040270	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv904204	chr15:50223697-50273670	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv904205	chr15:50228476-50286981	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12916154	GALK2	cis	parietal	SCAN
rs12916154	SLC12A1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50205400-50234400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr15:50226000-50245200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:50226400-50236000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:50228200-50234200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:50232400-50234200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr15:50232400-50241800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:50233000-50238800	Weak transcription	Primary monocytes fromperipheralblood	blood

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