Variant report

Variant	rs9877108
Chromosome Location	chr3:138538006-138538007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138536257..138538610-chr3:138539185..138541782,2	K562	blood:
2	chr3:138535838..138538762-chr3:138546948..138549872,2	K562	blood:

Extended variants
information (count: 121 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10804659	0.85[EUR][1000 genomes]
rs10935288	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705762	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11708762	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709768	0.84[EUR][1000 genomes]
rs11711360	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713049	0.86[EUR][1000 genomes]
rs11720178	0.92[EUR][1000 genomes]
rs11924479	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924814	0.86[EUR][1000 genomes]
rs12497815	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631035	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633714	0.82[EUR][1000 genomes]
rs13061496	0.80[EUR][1000 genomes]
rs13077455	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082808	0.87[EUR][1000 genomes]
rs1400266	0.86[EUR][1000 genomes]
rs168633	0.81[EUR][1000 genomes]
rs17484361	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191713	0.83[EUR][1000 genomes]
rs191714	0.84[EUR][1000 genomes]
rs191775	0.82[EUR][1000 genomes]
rs2197387	0.84[EUR][1000 genomes]
rs244380	0.83[EUR][1000 genomes]
rs28376988	0.83[EUR][1000 genomes]
rs28408150	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2881900	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35214574	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs361054	0.83[EUR][1000 genomes]
rs361059	0.82[EUR][1000 genomes]
rs361060	0.83[EUR][1000 genomes]
rs361061	0.83[EUR][1000 genomes]
rs361062	0.83[EUR][1000 genomes]
rs361066	0.84[EUR][1000 genomes]
rs361067	0.84[EUR][1000 genomes]
rs361068	0.84[EUR][1000 genomes]
rs361071	0.85[EUR][1000 genomes]
rs361072	0.84[EUR][1000 genomes]
rs361080	0.83[EUR][1000 genomes]
rs361081	0.83[EUR][1000 genomes]
rs361082	0.83[EUR][1000 genomes]
rs361083	0.83[EUR][1000 genomes]
rs361084	0.84[EUR][1000 genomes]
rs371762	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs385254	0.83[EUR][1000 genomes]
rs398065	0.85[EUR][1000 genomes]
rs404110	0.84[EUR][1000 genomes]
rs409507	0.83[EUR][1000 genomes]
rs413147	0.86[EUR][1000 genomes]
rs425901	0.81[EUR][1000 genomes]
rs4305444	0.83[EUR][1000 genomes]
rs439720	0.84[EUR][1000 genomes]
rs4405948	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473388	0.84[EUR][1000 genomes]
rs476800	0.84[EUR][1000 genomes]
rs482334	0.85[EUR][1000 genomes]
rs4894350	0.84[EUR][1000 genomes]
rs4894351	0.84[EUR][1000 genomes]
rs4894352	0.84[EUR][1000 genomes]
rs4894353	0.84[EUR][1000 genomes]
rs4894354	0.83[EUR][1000 genomes]
rs4894358	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894359	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491371	0.84[EUR][1000 genomes]
rs497900	0.82[EUR][1000 genomes]
rs500687	0.85[EUR][1000 genomes]
rs511207	0.84[EUR][1000 genomes]
rs539619	0.85[EUR][1000 genomes]
rs540198	0.84[EUR][1000 genomes]
rs540907	0.80[EUR][1000 genomes]
rs558905	0.85[EUR][1000 genomes]
rs559451	0.80[EUR][1000 genomes]
rs564455	0.85[EUR][1000 genomes]
rs607044	0.84[EUR][1000 genomes]
rs62282169	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6439817	0.83[EUR][1000 genomes]
rs6439819	0.82[EUR][1000 genomes]
rs647972	0.84[EUR][1000 genomes]
rs6773514	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776585	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6780989	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784610	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791627	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794270	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795203	0.81[EUR][1000 genomes]
rs6800801	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801207	0.86[EUR][1000 genomes]
rs6810351	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7612106	0.87[EUR][1000 genomes]
rs7613579	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628172	0.84[EUR][1000 genomes]
rs7643722	0.83[EUR][1000 genomes]
rs7646689	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650967	0.85[EUR][1000 genomes]
rs772612	0.83[EUR][1000 genomes]
rs9289566	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9647336	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647337	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813576	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817727	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818354	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9821694	0.85[EUR][1000 genomes]
rs9822500	0.82[EUR][1000 genomes]
rs9822714	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9823213	0.81[EUR][1000 genomes]
rs9832012	0.84[EUR][1000 genomes]
rs9834963	0.86[EUR][1000 genomes]
rs9853819	0.81[EUR][1000 genomes]
rs9855727	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9879784	0.92[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
rs9877108	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs9877108	FAIM	cis	Muscle Skeletal	GTEx
rs9877108	CEP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 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	chr3:138530600-138539200	Weak transcription	Fetal Intestine Small	intestine
14	chr3:138531200-138542600	Weak transcription	Fetal Stomach	stomach
15	chr3:138531800-138542800	Weak transcription	Osteobl	bone
16	chr3:138533200-138542600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:138535000-138538400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:138535000-138538800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:138535000-138543200	Weak transcription	Thymus	Thymus
20	chr3:138535000-138544000	Weak transcription	Fetal Thymus	thymus
21	chr3:138535000-138544200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:138535200-138538800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr3:138535200-138543600	Weak transcription	Dnd41	blood
24	chr3:138535200-138543800	Weak transcription	Primary T cells from cord blood	blood
25	chr3:138535200-138551600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:138536200-138538400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr3:138536200-138539200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:138536200-138539200	Enhancers	HepG2	liver
29	chr3:138536600-138538200	Enhancers	Right Atrium	heart
30	chr3:138536600-138538800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr3:138537000-138538200	Enhancers	Lung	lung
32	chr3:138537000-138552200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:138537200-138538600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:138537200-138543000	Weak transcription	Right Ventricle	heart
35	chr3:138537200-138544200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:138537200-138544200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:138537200-138548400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:138537200-138552000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:138537200-138552200	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:138537400-138538800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:138537400-138542000	Weak transcription	A549	lung
42	chr3:138537400-138542200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:138537400-138542200	Weak transcription	NHEK	skin
44	chr3:138537400-138542600	Weak transcription	Fetal Heart	heart
45	chr3:138537400-138543000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:138537400-138544000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:138537400-138544400	Weak transcription	Spleen	Spleen
48	chr3:138537400-138551400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:138537400-138552200	Weak transcription	Brain Anterior Caudate	brain
50	chr3:138537600-138538600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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