Variant report

Variant	rs28464790
Chromosome Location	chr3:56146554-56146555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10461036	0.92[EUR][1000 genomes]
rs10510779	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10510780	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10510781	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11428238	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13315826	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13326476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13326628	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17056469	0.96[EUR][1000 genomes]
rs17056472	0.95[EUR][1000 genomes]
rs17235263	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17235291	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17235305	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17235368	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17235375	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17235382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235396	0.88[EUR][1000 genomes]
rs17825159	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17825183	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17825189	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17825201	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17825207	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17825213	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17825219	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17825278	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1982766	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28463735	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35563958	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56101867	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58375176	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61401343	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6800841	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6807938	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73089299	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73091008	0.88[EUR][1000 genomes]
rs73091011	0.92[EUR][1000 genomes]
rs73091012	0.92[EUR][1000 genomes]
rs73091052	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73091061	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73091207	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73091213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73091231	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73091236	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73091241	0.89[EUR][1000 genomes]
rs73091242	0.85[EUR][1000 genomes]
rs7625220	0.94[EUR][1000 genomes]
rs7625230	0.93[EUR][1000 genomes]
rs7625422	0.92[EUR][1000 genomes]
rs7629639	0.89[EUR][1000 genomes]
rs7629769	0.95[EUR][1000 genomes]
rs7632887	0.94[EUR][1000 genomes]
rs7632901	0.94[EUR][1000 genomes]
rs7651932	0.91[EUR][1000 genomes]
rs923127	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs923128	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311594	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9311595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9311596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9810107	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9810354	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9811060	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811789	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9811790	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9814900	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9815611	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9817131	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9817492	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9817542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9819890	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9820348	0.86[EUR][1000 genomes]
rs9820493	0.95[EUR][1000 genomes]
rs9827514	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9828337	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830503	0.95[EUR][1000 genomes]
rs9831925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838245	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9842617	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844291	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9850438	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9854960	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9855148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9855836	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9857687	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9860909	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861486	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9862215	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865648	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9865958	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9866234	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9866951	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9869654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870248	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9870989	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9871223	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9880824	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881126	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881968	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9882373	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883636	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56144600-56152200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr3:56144800-56146600	Enhancers	H1 Cell Line	embryonic stem cell
3	chr3:56144800-56146600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:56144800-56146600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:56144800-56146800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:56144800-56147000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:56144800-56147000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr3:56144800-56148200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr3:56144800-56152400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:56145000-56146600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:56145000-56146600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:56145000-56146600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:56145000-56147000	Enhancers	Brain Germinal Matrix	brain
14	chr3:56145000-56147200	Enhancers	Fetal Lung	lung
15	chr3:56145400-56146600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:56145400-56147600	Weak transcription	Fetal Brain Male	brain
17	chr3:56145600-56147000	Enhancers	Fetal Stomach	stomach
18	chr3:56146000-56149200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:56146000-56151000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:56146200-56146600	Enhancers	NHDF-Ad	bronchial
21	chr3:56146400-56146600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr3:56146400-56148200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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