Variant report

Variant	rs2251746
Chromosome Location	chr1:159272060-159272061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10908709	1.00[YRI][hapmap]
rs12145079	0.82[YRI][hapmap]
rs12724895	0.81[MKK][hapmap];1.00[YRI][hapmap]
rs2247584	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2427836	0.90[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2427837	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494262	1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs2494264	1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2511214	1.00[YRI][hapmap]
rs2511215	0.81[AFR][1000 genomes]
rs6703348	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs863016	0.81[AMR][1000 genomes];0.83[EUR][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	nsv872487	chr1:159196765-159342439	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv872488	chr1:159218266-159336948	Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
IgE levels	22075330	GWAS catalog
IgE levels	18846228	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2251746	CD5L	cis	cerebellum	SCAN
rs2251746	PAQR6	cis	cerebellum	SCAN
rs2251746	SLAMF7	cis	parietal	SCAN
rs2251746	SUMO1P3	cis	parietal	SCAN
rs2251746	THBS3	cis	parietal	SCAN
rs2251746	EFNA1	cis	cerebellum	SCAN
rs2251746	FCER1A	cis	thalamus	BrainEAC
rs2251746	C1orf189	cis	cerebellum	SCAN
rs2251746	FCER1A	cis	brain	BrainEAC

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159271000-159274200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:159271400-159272200	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr1:159271800-159272200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr1:159271800-159272600	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:159272000-159272800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:159272000-159273200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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Input of quick search could be:

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

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