Variant report

Variant	rs4680249
Chromosome Location	chr3:155951279-155951280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1118418	0.93[ASN][1000 genomes]
rs1120745	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713991	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11915771	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11915832	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1353812	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1391889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1391890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499051	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499052	0.93[ASN][1000 genomes]
rs1499054	0.93[ASN][1000 genomes]
rs1499055	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs1499056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17170	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs1909372	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1909373	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1909374	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1909375	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1909376	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017971	0.83[AMR][1000 genomes]
rs2173492	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs4271877	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4333049	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4355235	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4450760	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4453801	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4472010	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4488791	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs4505650	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530487	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4533601	0.89[CEU][hapmap]
rs4577423	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4634068	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4679763	0.89[ASN][1000 genomes]
rs4679764	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679765	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs4680239	0.96[CEU][hapmap]
rs4680244	0.81[ASW][hapmap];0.85[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs4680248	0.81[AMR][1000 genomes]
rs6441039	0.89[CEU][hapmap]
rs6441042	0.82[CEU][hapmap]
rs6441045	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs6441046	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6441047	0.93[ASN][1000 genomes]
rs6441049	0.88[AMR][1000 genomes]
rs6441050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441051	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764861	0.85[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs6775600	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs6788238	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806129	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs728382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7372394	0.93[ASN][1000 genomes]
rs7373565	0.83[AMR][1000 genomes]
rs7611194	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7612532	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7620808	0.82[AMR][1000 genomes]
rs7621586	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7633871	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634800	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638421	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640712	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs963226	0.85[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs963227	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs9818040	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs9832745	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs9857202	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864967	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9866991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv592085	chr3:155827634-156012679	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4680249	SLC33A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155945800-155954400	Weak transcription	Pancreas	Pancrea
2	chr3:155951000-155952000	Enhancers	Aorta	Aorta
3	chr3:155951000-155952400	Enhancers	NHEK	skin
4	chr3:155951000-155952600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:155951000-155953200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:155951200-155951600	Enhancers	Placenta	Placenta
7	chr3:155951200-155951800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:155951200-155952000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:155951200-155952000	Enhancers	Placenta Amnion	Placenta Amnion
10	chr3:155951200-155952200	Enhancers	HMEC	breast

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