Variant report

Variant	rs1880662
Chromosome Location	chr3:143336797-143336798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10513212	1.00[CEU][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11915862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061355	1.00[ASW][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13074668	0.81[JPT][hapmap]
rs13074737	0.88[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs13076528	0.81[JPT][hapmap]
rs13076949	1.00[ASW][hapmap]
rs13082568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084941	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1525858	1.00[ASW][hapmap]
rs16853857	1.00[ASW][hapmap]
rs17640925	1.00[ASW][hapmap]
rs2030818	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34210617	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34225320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34467389	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35152294	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35175368	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35629124	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839601	1.00[ASW][hapmap]
rs4839602	1.00[ASW][hapmap]
rs4839603	0.81[JPT][hapmap]
rs4839647	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73152833	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746055	1.00[ASW][hapmap]
rs9841219	1.00[ASW][hapmap]

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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1880662	GK5	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143297600-143339000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:143300400-143336800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:143324200-143340000	Weak transcription	Primary B cells from cord blood	blood
4	chr3:143324400-143353800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:143328200-143376200	Weak transcription	Ovary	ovary
6	chr3:143328400-143346000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:143329600-143337200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:143332600-143337200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:143335600-143337400	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:143336600-143336800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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