Variant report

Variant	rs16963064
Chromosome Location	chr15:50208667-50208668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10519246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519248	1.00[ASN][1000 genomes]
rs12101710	1.00[ASN][1000 genomes]
rs12101847	1.00[ASN][1000 genomes]
rs12899404	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904852	1.00[ASN][1000 genomes]
rs12905192	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905409	1.00[ASN][1000 genomes]
rs12907398	1.00[ASN][1000 genomes]
rs12916154	1.00[ASN][1000 genomes]
rs13329614	1.00[ASN][1000 genomes]
rs16953000	0.97[GIH][hapmap];0.90[TSI][hapmap]
rs16963032	1.00[ASN][1000 genomes]
rs16963056	1.00[ASN][1000 genomes]
rs16963067	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963076	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963083	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17495375	0.90[GIH][hapmap]
rs2413979	1.00[ASN][1000 genomes]
rs28406046	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28412330	1.00[ASN][1000 genomes]
rs28416417	1.00[ASN][1000 genomes]
rs28437808	1.00[ASN][1000 genomes]
rs28502034	1.00[ASN][1000 genomes]
rs28555213	1.00[ASN][1000 genomes]
rs28627943	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640908	1.00[ASN][1000 genomes]
rs28649135	1.00[ASN][1000 genomes]
rs28669725	1.00[ASN][1000 genomes]
rs28687946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28698041	1.00[ASN][1000 genomes]
rs28699236	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28756960	1.00[ASN][1000 genomes]
rs28809909	1.00[ASN][1000 genomes]
rs28823045	1.00[ASN][1000 genomes]
rs28836239	1.00[ASN][1000 genomes]
rs28837213	1.00[ASN][1000 genomes]
rs28844958	1.00[ASN][1000 genomes]
rs28856727	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	1.00[ASN][1000 genomes]
rs4407015	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426299	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4491453	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183166	1.00[ASN][1000 genomes]
rs74012838	1.00[ASN][1000 genomes]
rs74012843	1.00[ASN][1000 genomes]
rs7496373	1.00[ASN][1000 genomes]
rs8040270	1.00[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16963064	SERINC4	cis	cerebellum	SCAN
rs16963064	SLC27A2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50161800-50210600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:50201000-50209400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr15:50202600-50217600	Weak transcription	Liver	Liver
4	chr15:50205400-50234400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:50207200-50217400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr15:50207800-50216400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:50208400-50209000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:50208400-50209600	Genic enhancers	Primary hematopoietic stem cells	blood
9	chr15:50208400-50210800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:50208600-50208800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr15:50208600-50211400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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