Variant report

Variant	rs540907
Chromosome Location	chr3:138465360-138465361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138453648..138456326-chr3:138462764..138465635,2	K562	blood:
2	chr3:138464471..138467616-chr3:138469516..138472812,3	K562	blood:
3	chr3:138464449..138466170-chr3:138471312..138473227,2	K562	blood:

Extended variants
information (count: 138 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1066197	0.86[EUR][1000 genomes]
rs1068104	0.87[EUR][1000 genomes]
rs1068685	0.88[EUR][1000 genomes]
rs11705762	0.93[EUR][1000 genomes]
rs11709768	0.94[EUR][1000 genomes]
rs11713049	0.94[EUR][1000 genomes]
rs11717457	0.91[EUR][1000 genomes]
rs11720178	0.87[EUR][1000 genomes]
rs11924814	0.94[EUR][1000 genomes]
rs13069296	0.88[EUR][1000 genomes]
rs13082808	0.93[EUR][1000 genomes]
rs13433948	0.84[EUR][1000 genomes]
rs1400266	0.94[EUR][1000 genomes]
rs1663556	0.88[EUR][1000 genomes]
rs1673597	0.88[EUR][1000 genomes]
rs168633	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs181729	0.88[EUR][1000 genomes]
rs187245	0.80[EUR][1000 genomes]
rs191713	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs191714	0.92[EUR][1000 genomes]
rs191775	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2197387	0.95[EUR][1000 genomes]
rs2348147	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs244380	0.93[EUR][1000 genomes]
rs244381	0.93[EUR][1000 genomes]
rs2595928	0.86[EUR][1000 genomes]
rs2595930	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2607796	0.87[EUR][1000 genomes]
rs28376988	0.93[EUR][1000 genomes]
rs28408150	0.93[EUR][1000 genomes]
rs34354181	0.81[EUR][1000 genomes]
rs35214574	0.90[EUR][1000 genomes]
rs361054	0.94[EUR][1000 genomes]
rs361056	0.91[AFR][1000 genomes]
rs361057	0.87[EUR][1000 genomes]
rs361059	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs361060	0.93[EUR][1000 genomes]
rs361061	0.93[EUR][1000 genomes]
rs361062	0.93[EUR][1000 genomes]
rs361063	0.89[EUR][1000 genomes]
rs361064	0.89[AFR][1000 genomes]
rs361066	0.95[EUR][1000 genomes]
rs361067	0.95[EUR][1000 genomes]
rs361068	0.95[EUR][1000 genomes]
rs361069	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs361071	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs361072	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs361079	0.90[AFR][1000 genomes]
rs361080	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361081	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361082	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361083	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs361084	0.92[EUR][1000 genomes]
rs361088	0.88[EUR][1000 genomes]
rs361089	0.87[EUR][1000 genomes]
rs361092	0.88[EUR][1000 genomes]
rs361094	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs361097	0.88[EUR][1000 genomes]
rs371762	0.93[EUR][1000 genomes]
rs385254	0.93[EUR][1000 genomes]
rs398065	0.95[EUR][1000 genomes]
rs404110	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs409507	0.93[EUR][1000 genomes]
rs413147	0.94[EUR][1000 genomes]
rs425901	0.93[EUR][1000 genomes]
rs4305444	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs439720	0.92[EUR][1000 genomes]
rs448808	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs470359	0.88[EUR][1000 genomes]
rs473388	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs475254	0.88[EUR][1000 genomes]
rs476800	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs482334	0.95[EUR][1000 genomes]
rs4894350	0.95[EUR][1000 genomes]
rs4894351	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4894352	0.95[EUR][1000 genomes]
rs4894353	0.92[EUR][1000 genomes]
rs4894354	0.90[EUR][1000 genomes]
rs491371	0.94[EUR][1000 genomes]
rs497900	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs500687	0.95[EUR][1000 genomes]
rs511207	0.94[EUR][1000 genomes]
rs524164	0.88[EUR][1000 genomes]
rs539156	0.88[EUR][1000 genomes]
rs539619	0.95[EUR][1000 genomes]
rs540198	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs550768	0.87[EUR][1000 genomes]
rs558905	0.95[EUR][1000 genomes]
rs559160	0.88[EUR][1000 genomes]
rs559451	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs564455	0.95[EUR][1000 genomes]
rs589986	0.87[EUR][1000 genomes]
rs603723	0.88[EUR][1000 genomes]
rs607044	0.96[EUR][1000 genomes]
rs618457	0.85[EUR][1000 genomes]
rs621204	0.87[EUR][1000 genomes]
rs62282169	0.87[EUR][1000 genomes]
rs624099	0.88[EUR][1000 genomes]
rs625468	0.88[EUR][1000 genomes]
rs635592	0.88[EUR][1000 genomes]
rs6439817	0.93[EUR][1000 genomes]
rs6439819	0.93[EUR][1000 genomes]
rs647972	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6776585	0.93[EUR][1000 genomes]
rs6781914	0.85[EUR][1000 genomes]
rs6784610	0.80[EUR][1000 genomes]
rs6794270	0.81[EUR][1000 genomes]
rs6795203	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6801207	0.94[EUR][1000 genomes]
rs6810351	0.93[EUR][1000 genomes]
rs7612106	0.93[EUR][1000 genomes]
rs7615854	0.82[AFR][1000 genomes]
rs7643722	0.93[EUR][1000 genomes]
rs772612	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs773045	0.88[EUR][1000 genomes]
rs773184	0.87[EUR][1000 genomes]
rs9821694	0.95[EUR][1000 genomes]
rs9822714	0.95[EUR][1000 genomes]
rs9823213	0.93[EUR][1000 genomes]
rs9832012	0.94[EUR][1000 genomes]
rs9834963	0.94[EUR][1000 genomes]
rs9853819	0.95[EUR][1000 genomes]
rs9863481	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9864176	0.88[EUR][1000 genomes]
rs9874723	0.81[EUR][1000 genomes]
rs9877108	0.80[EUR][1000 genomes]
rs9879784	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs540907	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs540907	CEP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138369000-138493000	Weak transcription	Fetal Lung	lung
2	chr3:138393800-138515000	Weak transcription	Aorta	Aorta
3	chr3:138395800-138480200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:138396000-138469200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:138396200-138469200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:138396200-138486400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:138396200-138487000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:138408000-138479800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:138408400-138499200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:138413800-138487600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:138416200-138469400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:138416800-138486600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:138417800-138486600	Weak transcription	Hela-S3	cervix
14	chr3:138419000-138487000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:138419200-138486200	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:138421800-138479800	Weak transcription	Small Intestine	intestine
17	chr3:138423400-138469400	Weak transcription	A549	lung
18	chr3:138423400-138487000	Weak transcription	Colonic Mucosa	Colon
19	chr3:138432400-138469200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:138438600-138486400	Weak transcription	Esophagus	oesophagus
21	chr3:138440600-138470800	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:138443000-138483200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:138443600-138467200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:138443800-138469200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:138443800-138474400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:138444600-138468600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:138445000-138478000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:138445800-138469400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:138446000-138486200	Weak transcription	GM12878-XiMat	blood
30	chr3:138446200-138483600	Weak transcription	NH-A	brain
31	chr3:138446400-138471800	Weak transcription	NHEK	skin
32	chr3:138451600-138469200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:138452400-138473400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:138453800-138469200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:138454400-138486400	Weak transcription	HSMM	muscle
36	chr3:138455200-138486400	Weak transcription	Spleen	Spleen
37	chr3:138458600-138466800	Weak transcription	Fetal Brain Male	brain
38	chr3:138459800-138468800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:138459800-138469200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:138459800-138482800	Weak transcription	Lung	lung
41	chr3:138459800-138483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:138460200-138468800	Weak transcription	Pancreas	Pancrea
43	chr3:138460200-138469200	Weak transcription	Fetal Brain Female	brain
44	chr3:138460200-138486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:138460200-138486400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:138460400-138468800	Weak transcription	Fetal Intestine Large	intestine
47	chr3:138460400-138469200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:138460400-138469200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:138460400-138469200	Weak transcription	Fetal Thymus	thymus
50	chr3:138460400-138473400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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