Variant report

Variant	rs2032172
Chromosome Location	chr21:40244834-40244835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10854390	0.82[ASN][1000 genomes]
rs12481753	0.81[ASN][1000 genomes]
rs12482288	0.82[ASN][1000 genomes]
rs12483491	0.82[ASN][1000 genomes]
rs13048952	0.82[ASN][1000 genomes]
rs13050477	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs13051097	0.82[ASN][1000 genomes]
rs1475592	0.83[CEU][hapmap]
rs2032171	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094873	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2150409	0.84[CEU][hapmap];0.91[MEX][hapmap]
rs2210265	0.86[MEX][hapmap]
rs2836718	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2836719	0.82[ASN][1000 genomes]
rs2836722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836723	0.84[CEU][hapmap];0.91[MEX][hapmap]
rs2836725	0.83[CEU][hapmap]
rs2836735	0.81[CHB][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs2836737	0.86[GIH][hapmap]
rs2836740	0.81[ASN][1000 genomes]
rs4143382	0.99[ASN][1000 genomes]
rs4432550	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467788	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs468042	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs468637	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs469043	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs469368	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs469443	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469524	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4817966	0.82[ASN][1000 genomes]
rs7275685	0.82[ASN][1000 genomes]
rs7276441	0.82[ASN][1000 genomes]
rs7277330	0.82[ASN][1000 genomes]
rs7279223	0.82[ASN][1000 genomes]
rs7279660	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8126904	0.81[ASN][1000 genomes]
rs8131220	0.82[ASN][1000 genomes]
rs9653664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9680142	0.82[ASN][1000 genomes]
rs9680143	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs992242	0.84[CEU][hapmap];0.91[MEX][hapmap]
rs992243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv587478	chr21:40243459-40275033	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2032172	FAM19A4	trans	cerebellum	SCAN
rs2032172	PCP4	cis	cerebellum	SCAN
rs2032172	TUBB2C	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40229600-40245400	Weak transcription	Left Ventricle	heart
2	chr21:40233600-40245400	Weak transcription	Right Atrium	heart
3	chr21:40235600-40247600	Weak transcription	Spleen	Spleen
4	chr21:40241600-40246600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr21:40242200-40246600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr21:40242200-40246600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr21:40242200-40247600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr21:40243000-40246600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr21:40244800-40247200	Weak transcription	Thymus	Thymus

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