Variant report

Variant	rs2427828
Chromosome Location	chr1:159273041-159273042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11265186	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11265187	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11265193	1.00[YRI][hapmap]
rs12118628	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs12145616	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2252226	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2254681	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2427824	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs2427825	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs2427827	0.90[ASN][1000 genomes]
rs2494250	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494258	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2494260	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2494261	0.87[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2494263	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2494265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511212	0.82[ASW][hapmap];0.94[CHB][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4128725	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4269772	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs863012	0.88[AFR][1000 genomes]
rs863017	0.88[AFR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2427828	CD1D	cis	cerebellum	SCAN
rs2427828	FCER1A	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159271000-159274200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:159272000-159273200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:159272600-159273800	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr1:159272600-159277000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:159273000-159273200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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