Variant report

Variant	rs16863323
Chromosome Location	chr3:151060068-151060069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1048408	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10513392	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1125541	0.90[CEU][hapmap]
rs11714714	0.84[ASN][1000 genomes]
rs11715892	0.90[CEU][hapmap]
rs11717955	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs11719936	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12330831	0.84[ASN][1000 genomes]
rs12487835	0.85[CEU][hapmap]
rs12488267	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12492699	0.90[CEU][hapmap]
rs12494865	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317465	0.83[ASN][1000 genomes]
rs1352886	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388628	0.90[CEU][hapmap]
rs1463725	0.82[LWK][hapmap];0.88[MKK][hapmap]
rs1472122	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1565574	0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.96[ASN][1000 genomes]
rs16863334	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16863336	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1844924	0.94[ASN][1000 genomes]
rs1882014	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1882015	0.84[ASN][1000 genomes]
rs1882016	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1882017	0.84[ASN][1000 genomes]
rs1920396	0.84[ASN][1000 genomes]
rs28371419	0.94[ASN][1000 genomes]
rs28497341	0.95[ASN][1000 genomes]
rs2904430	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3971192	0.90[CEU][hapmap]
rs4076581	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[EUR][1000 genomes]
rs4475010	0.81[ASN][1000 genomes]
rs4679783	0.83[ASN][1000 genomes]
rs56105302	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56367650	0.86[ASN][1000 genomes]
rs58334126	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62283021	0.87[ASN][1000 genomes]
rs6765215	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768130	0.86[ASN][1000 genomes]
rs6782313	0.84[ASN][1000 genomes]
rs6793061	0.85[CEU][hapmap]
rs6807308	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7617677	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[ASN][1000 genomes]
rs7621113	0.84[ASN][1000 genomes]
rs7621183	0.84[ASN][1000 genomes]
rs7621211	0.84[ASN][1000 genomes]
rs7623448	0.84[ASN][1000 genomes]
rs7653603	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8180086	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[ASN][1000 genomes]
rs9757688	0.84[ASN][1000 genomes]
rs9810067	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs9827619	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[ASN][1000 genomes]
rs9828553	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9829753	0.85[ASN][1000 genomes]
rs9870740	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9875152	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16863323	SLC33A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151045600-151063600	Weak transcription	Brain Angular Gyrus	brain
2	chr3:151050000-151063600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:151057000-151063200	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:151058800-151063600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:151059000-151062800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:151059000-151062800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:151059200-151061800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:151059200-151063400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:151059200-151063600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:151059200-151063800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:151059400-151064200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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