Variant report

Variant	rs1877222
Chromosome Location	chr3:140938546-140938547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13069904	0.96[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1511371	0.83[EUR][1000 genomes]
rs1511372	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1511373	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2048459	0.85[EUR][1000 genomes]
rs2291039	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683585	0.85[EUR][1000 genomes]
rs4683586	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs6779870	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7613113	0.83[EUR][1000 genomes]
rs7652530	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs967526	0.90[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9875630	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1877222	XRN1	cis	parietal	SCAN
rs1877222	ACPL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140931800-140941200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:140935800-140938800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:140936400-140940000	Enhancers	Fetal Heart	heart
4	chr3:140937200-140940600	Weak transcription	Right Atrium	heart
5	chr3:140937600-140938600	Weak transcription	Left Ventricle	heart
6	chr3:140937600-140946800	Weak transcription	Thymus	Thymus
7	chr3:140937800-140938800	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr3:140938000-140938600	Enhancers	Fetal Brain Male	brain
9	chr3:140938200-140940000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:140938400-140939000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:140938400-140939200	Enhancers	Primary neutrophils fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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