Variant report

Variant	rs28376988
Chromosome Location	chr3:138435863-138435864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 151 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1066197	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1068104	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1068685	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11705762	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709768	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713049	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717457	0.90[EUR][1000 genomes]
rs11720178	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924814	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069296	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13082808	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433948	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1400266	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663554	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1663556	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673597	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs168633	0.94[EUR][1000 genomes]
rs181729	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs187245	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191713	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191714	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191775	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2197387	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348147	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs244380	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244381	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2595928	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2595930	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595932	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607108	0.89[ASN][1000 genomes]
rs2607109	0.89[ASN][1000 genomes]
rs2607796	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28408150	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34900559	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35214574	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361054	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361055	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361056	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361057	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361059	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361060	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361061	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs361062	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361063	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361064	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361065	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361066	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361067	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361068	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361069	0.88[EUR][1000 genomes]
rs361071	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361072	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361079	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361080	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361081	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361082	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361083	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361084	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361085	0.89[ASN][1000 genomes]
rs361086	0.81[EUR][1000 genomes]
rs361087	0.80[EUR][1000 genomes]
rs361088	0.93[EUR][1000 genomes]
rs361089	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs361092	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs361094	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361096	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361097	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371762	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385254	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398065	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404110	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409507	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413147	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425901	0.93[EUR][1000 genomes]
rs4305444	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439720	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs448808	0.92[EUR][1000 genomes]
rs470359	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs473388	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475254	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs476800	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482334	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894350	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894351	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894352	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894353	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894354	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491371	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs493152	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497900	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500687	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511207	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs524164	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531577	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539156	0.91[EUR][1000 genomes]
rs539619	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540198	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540907	0.93[EUR][1000 genomes]
rs550768	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs558905	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559160	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs559451	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs564455	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574942	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589986	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603723	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs607044	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618457	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs621204	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62282169	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624099	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs625468	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635592	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6439817	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439819	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs647972	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs654459	0.86[EUR][1000 genomes]
rs6776585	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781914	0.88[EUR][1000 genomes]
rs6784610	0.83[EUR][1000 genomes]
rs6794270	0.84[EUR][1000 genomes]
rs6795203	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6801207	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810351	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7612106	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643722	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772612	0.96[EUR][1000 genomes]
rs773045	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs773184	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9818354	0.80[EUR][1000 genomes]
rs9821694	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822714	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823213	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9832012	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834963	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853819	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9863481	0.87[EUR][1000 genomes]
rs9864176	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874723	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877108	0.83[EUR][1000 genomes]
rs9879784	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28376988	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs28376988	FAIM	cis	Muscle Skeletal	GTEx
rs28376988	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138364400-138459200	Weak transcription	Psoas Muscle	Psoas
2	chr3:138369000-138493000	Weak transcription	Fetal Lung	lung
3	chr3:138383200-138448200	Weak transcription	Gastric	stomach
4	chr3:138383400-138443000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:138390800-138459600	Weak transcription	Right Ventricle	heart
6	chr3:138393800-138515000	Weak transcription	Aorta	Aorta
7	chr3:138395200-138436800	Weak transcription	Brain Germinal Matrix	brain
8	chr3:138395800-138444800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:138395800-138459800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:138395800-138480200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:138396000-138436400	Weak transcription	Fetal Brain Female	brain
12	chr3:138396000-138469200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:138396200-138443200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:138396200-138469200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:138396200-138486400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:138396200-138487000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:138399600-138443400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:138400600-138442800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:138401600-138436600	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:138401800-138442800	Weak transcription	Brain Angular Gyrus	brain
21	chr3:138402000-138442800	Weak transcription	Brain Substantia Nigra	brain
22	chr3:138404800-138442200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:138406800-138442200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:138408000-138479800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:138408200-138443200	Weak transcription	Brain Anterior Caudate	brain
26	chr3:138408400-138499200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:138413800-138445400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:138413800-138445400	Weak transcription	Ovary	ovary
29	chr3:138413800-138458400	Weak transcription	Thymus	Thymus
30	chr3:138413800-138487600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:138414200-138453400	Weak transcription	HMEC	breast
32	chr3:138414400-138436200	Weak transcription	NHDF-Ad	bronchial
33	chr3:138415800-138445800	Weak transcription	NH-A	brain
34	chr3:138416200-138443200	Weak transcription	Fetal Heart	heart
35	chr3:138416200-138469400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:138416600-138459400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:138416800-138439400	Weak transcription	Lung	lung
38	chr3:138416800-138486600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:138417000-138458800	Weak transcription	Pancreas	Pancrea
40	chr3:138417800-138486600	Weak transcription	Hela-S3	cervix
41	chr3:138418400-138459200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:138419000-138487000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:138419200-138442000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:138419200-138442200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:138419200-138450400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:138419200-138486200	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:138419600-138442800	Weak transcription	HUVEC	blood vessel
48	chr3:138421800-138479800	Weak transcription	Small Intestine	intestine
49	chr3:138422200-138441000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:138423000-138438800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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