Variant report

Variant	rs9818354
Chromosome Location	chr3:138541239-138541240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:138541145-138541415	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:138525639..138527361-chr3:138540690..138543312,2	K562	blood:
2	chr3:138536257..138538610-chr3:138539185..138541782,2	K562	blood:
3	chr3:138539146..138542013-chr3:138544348..138547069,3	K562	blood:
4	chr3:138539568..138542251-chr3:138633369..138635951,2	K562	blood:

Variant related genes	Relation type
EEF1A1P25	TF binding region

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10804659	0.86[EUR][1000 genomes]
rs10935288	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11705762	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11706016	0.81[EUR][1000 genomes]
rs11708762	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11709768	0.81[EUR][1000 genomes]
rs11711360	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11713049	0.84[EUR][1000 genomes]
rs11720178	0.89[EUR][1000 genomes]
rs11924479	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11924814	0.84[EUR][1000 genomes]
rs12497815	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12631035	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12633714	0.84[EUR][1000 genomes]
rs13061496	0.82[EUR][1000 genomes]
rs13077455	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13082808	0.85[EUR][1000 genomes]
rs1400266	0.84[EUR][1000 genomes]
rs17484361	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs191713	0.80[EUR][1000 genomes]
rs191714	0.81[EUR][1000 genomes]
rs2197387	0.82[EUR][1000 genomes]
rs244380	0.80[EUR][1000 genomes]
rs28376988	0.80[EUR][1000 genomes]
rs28408150	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2881900	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35214574	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs361054	0.83[EUR][1000 genomes]
rs361060	0.80[EUR][1000 genomes]
rs361061	0.80[EUR][1000 genomes]
rs361062	0.80[EUR][1000 genomes]
rs361066	0.82[EUR][1000 genomes]
rs361067	0.82[EUR][1000 genomes]
rs361068	0.82[EUR][1000 genomes]
rs361071	0.82[EUR][1000 genomes]
rs361072	0.82[EUR][1000 genomes]
rs361080	0.81[EUR][1000 genomes]
rs361081	0.81[EUR][1000 genomes]
rs361082	0.81[EUR][1000 genomes]
rs361083	0.81[EUR][1000 genomes]
rs361084	0.81[EUR][1000 genomes]
rs371762	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs385254	0.80[EUR][1000 genomes]
rs398065	0.82[EUR][1000 genomes]
rs404110	0.82[EUR][1000 genomes]
rs409507	0.80[EUR][1000 genomes]
rs413147	0.84[EUR][1000 genomes]
rs4305444	0.81[EUR][1000 genomes]
rs439720	0.81[EUR][1000 genomes]
rs4405948	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs473388	0.82[EUR][1000 genomes]
rs476800	0.82[EUR][1000 genomes]
rs482334	0.82[EUR][1000 genomes]
rs4894350	0.82[EUR][1000 genomes]
rs4894351	0.81[EUR][1000 genomes]
rs4894352	0.82[EUR][1000 genomes]
rs4894353	0.81[EUR][1000 genomes]
rs4894354	0.81[EUR][1000 genomes]
rs4894358	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4894359	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs491371	0.81[EUR][1000 genomes]
rs500687	0.82[EUR][1000 genomes]
rs511207	0.81[EUR][1000 genomes]
rs539619	0.82[EUR][1000 genomes]
rs540198	0.81[EUR][1000 genomes]
rs558905	0.82[EUR][1000 genomes]
rs564455	0.82[EUR][1000 genomes]
rs607044	0.82[EUR][1000 genomes]
rs62282169	0.84[EUR][1000 genomes]
rs6439817	0.80[EUR][1000 genomes]
rs647972	0.82[EUR][1000 genomes]
rs6773514	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6776585	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6780989	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6784610	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6791627	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6794270	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6800801	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6801207	0.84[EUR][1000 genomes]
rs6810351	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7612106	0.84[EUR][1000 genomes]
rs7613579	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7628172	0.86[EUR][1000 genomes]
rs7643722	0.80[EUR][1000 genomes]
rs7646689	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7650967	0.86[EUR][1000 genomes]
rs772612	0.81[EUR][1000 genomes]
rs9289566	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9647336	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9647337	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9813576	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9817727	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9821694	0.82[EUR][1000 genomes]
rs9822500	0.84[EUR][1000 genomes]
rs9822714	0.82[EUR][1000 genomes]
rs9832012	0.81[EUR][1000 genomes]
rs9834963	0.84[EUR][1000 genomes]
rs9855727	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9877108	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9879784	0.90[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9818354	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs9818354	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs9818354	FAIM	cis	Muscle Skeletal	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138504000-138552000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:138506000-138542200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:138506000-138551800	Weak transcription	Primary B cells from cord blood	blood
4	chr3:138512000-138542800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:138513400-138544400	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:138513800-138543000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:138513800-138543000	Weak transcription	Placenta	Placenta
8	chr3:138514800-138542600	Weak transcription	Hela-S3	cervix
9	chr3:138523000-138542600	Weak transcription	HMEC	breast
10	chr3:138523000-138543000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:138528800-138552600	Weak transcription	Colonic Mucosa	Colon
12	chr3:138529400-138544400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:138531200-138542600	Weak transcription	Fetal Stomach	stomach
14	chr3:138531800-138542800	Weak transcription	Osteobl	bone
15	chr3:138533200-138542600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:138535000-138543200	Weak transcription	Thymus	Thymus
17	chr3:138535000-138544000	Weak transcription	Fetal Thymus	thymus
18	chr3:138535000-138544200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:138535200-138543600	Weak transcription	Dnd41	blood
20	chr3:138535200-138543800	Weak transcription	Primary T cells from cord blood	blood
21	chr3:138535200-138551600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:138537000-138552200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:138537200-138543000	Weak transcription	Right Ventricle	heart
24	chr3:138537200-138544200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:138537200-138544200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:138537200-138548400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:138537200-138552000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:138537200-138552200	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:138537400-138542000	Weak transcription	A549	lung
30	chr3:138537400-138542200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:138537400-138542200	Weak transcription	NHEK	skin
32	chr3:138537400-138542600	Weak transcription	Fetal Heart	heart
33	chr3:138537400-138543000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:138537400-138544000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:138537400-138544400	Weak transcription	Spleen	Spleen
36	chr3:138537400-138551400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:138537400-138552200	Weak transcription	Brain Anterior Caudate	brain
38	chr3:138537600-138542600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:138537600-138542600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:138537600-138542600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:138537600-138542600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:138537600-138542600	Weak transcription	Adipose Nuclei	Adipose
43	chr3:138537600-138542600	Weak transcription	Fetal Intestine Large	intestine
44	chr3:138537600-138542600	Weak transcription	HUVEC	blood vessel
45	chr3:138537600-138542800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:138537600-138542800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:138537600-138543000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:138537600-138543000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:138537600-138543000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:138537600-138543000	Weak transcription	Left Ventricle	heart

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