Variant report

Variant	rs4682399
Chromosome Location	chr3:112044781-112044782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10511311	0.80[CEU][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes]
rs12106673	0.88[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs12106967	0.88[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs13069751	0.98[EUR][1000 genomes]
rs13069935	0.97[EUR][1000 genomes]
rs13070091	0.98[EUR][1000 genomes]
rs13072567	0.87[AMR][1000 genomes]
rs13092081	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13095299	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13098589	0.80[CEU][hapmap];0.84[MEX][hapmap]
rs13100916	0.81[EUR][1000 genomes]
rs1317243	0.92[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs1879513	0.98[EUR][1000 genomes]
rs2272022	0.80[CEU][hapmap];0.84[MEX][hapmap]
rs2276772	0.88[AMR][1000 genomes]
rs2399412	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2399416	0.80[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs4682398	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438064	0.97[EUR][1000 genomes]
rs6438065	0.98[EUR][1000 genomes]
rs6762106	0.98[EUR][1000 genomes]
rs6773206	0.98[EUR][1000 genomes]
rs6780745	0.96[EUR][1000 genomes]
rs6798354	0.98[EUR][1000 genomes]
rs6798486	0.98[EUR][1000 genomes]
rs6805117	0.98[EUR][1000 genomes]
rs6805142	0.93[EUR][1000 genomes]
rs7647411	0.80[CEU][hapmap];0.84[MEX][hapmap]
rs8179893	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8179913	0.97[EUR][1000 genomes]
rs9814721	0.98[EUR][1000 genomes]
rs9837466	0.94[CHB][hapmap]
rs9852176	0.98[EUR][1000 genomes]
rs9856838	0.98[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	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
rs4682399	CD200	cis	parietal	SCAN
rs4682399	CD200	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112038400-112045200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:112041400-112045600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:112041400-112045600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:112041400-112045800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:112041400-112050600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:112041400-112050800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:112041600-112045600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:112041600-112045600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:112044200-112044800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:112044200-112044800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:112044400-112045600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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