Variant report

Variant	rs2820974
Chromosome Location	chr1:47893929-47893930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10399673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11577621	0.83[TSI][hapmap]
rs11578776	0.82[TSI][hapmap]
rs12070024	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12090153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1316443	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1680020	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2405922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2622909	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622917	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820970	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2820971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738315	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4603175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527551	0.82[AMR][1000 genomes]
rs55718554	0.92[EUR][1000 genomes]
rs557851	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs571281	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61103903	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6673882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6673934	0.91[EUR][1000 genomes]
rs7525184	0.88[GIH][hapmap];0.85[TSI][hapmap]
rs7552140	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9436899	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534956	chr1:47882277-47905486	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2820974	CYP4Z2P	cis	cerebellum	SCAN
rs2820974	CMPK1	cis	parietal	SCAN
rs2820974	HECTD3	cis	parietal	SCAN
rs2820974	CMPK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47882800-47898400	Weak transcription	Aorta	Aorta
2	chr1:47885800-47897800	Weak transcription	Colonic Mucosa	Colon
3	chr1:47889800-47894000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:47890000-47896600	Weak transcription	A549	lung
5	chr1:47890200-47897000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:47890200-47897200	Weak transcription	K562	blood
7	chr1:47890400-47898000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:47890600-47897000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:47891000-47896600	Weak transcription	Dnd41	blood
10	chr1:47891400-47896800	Weak transcription	Fetal Intestine Small	intestine
11	chr1:47891400-47897000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:47892800-47896800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:47893200-47897200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:47893400-47894000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:47893600-47898200	Weak transcription	Hela-S3	cervix

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