Variant report

Variant	rs9845940
Chromosome Location	chr3:146499301-146499302
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1003263	0.95[ASN][1000 genomes]
rs1003264	0.95[ASN][1000 genomes]
rs1019897	0.99[ASN][1000 genomes]
rs10935642	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10935643	0.87[ASN][1000 genomes]
rs11705960	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497166	0.88[ASN][1000 genomes]
rs1549838	0.99[ASN][1000 genomes]
rs1606177	0.88[ASN][1000 genomes]
rs1606178	0.88[ASN][1000 genomes]
rs17371141	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17701818	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991715	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28493260	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28624889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28885973	0.88[ASN][1000 genomes]
rs3843364	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681336	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55895997	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56887948	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58890956	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272988	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440455	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440458	0.97[ASN][1000 genomes]
rs6440459	0.99[ASN][1000 genomes]
rs6440460	0.99[ASN][1000 genomes]
rs6762735	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6781142	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6808136	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619766	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638634	0.88[ASN][1000 genomes]
rs9289731	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289732	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs961897	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs981484	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828677	0.94[ASN][1000 genomes]
rs9831862	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9834967	0.95[ASN][1000 genomes]
rs9835606	0.95[ASN][1000 genomes]
rs9840734	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9841610	0.99[ASN][1000 genomes]
rs9841625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841883	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842074	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9856265	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857850	0.96[ASN][1000 genomes]
rs9861781	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861946	0.99[ASN][1000 genomes]
rs9862944	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516386	chr3:146366513-146758405	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591961	chr3:146394094-146725217	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1007875	chr3:146401461-146776618	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv877624	chr3:146414837-146536741	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv998040	chr3:146416916-146729962	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv536760	chr3:146416916-146729962	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1001931	chr3:146419061-146745361	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv877625	chr3:146461435-146521978	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9845940	TSC22D2	cis	parietal	SCAN
rs9845940	PLSCR1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146497400-146500200	Enhancers	Muscle Satellite Cultured Cells	--
2	chr3:146498600-146499400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:146498600-146501400	Enhancers	NHDF-Ad	bronchial
4	chr3:146498800-146499400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:146498800-146499400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:146498800-146499600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:146498800-146499800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:146498800-146499800	Enhancers	Colon Smooth Muscle	Colon
9	chr3:146498800-146500800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:146498800-146501000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:146499000-146499400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr3:146499000-146500800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:146499200-146499400	Flanking Active TSS	Osteobl	bone
14	chr3:146499200-146499600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:146499200-146499600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr3:146499200-146500800	Weak transcription	Ovary	ovary
17	chr3:146499200-146501600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:146499200-146503400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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