Variant report

Variant	rs361087
Chromosome Location	chr3:138383144-138383145
allele	A/C
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	chr3:138383114-138383152	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:138382501-138385824	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138312928..138314956-chr3:138381208..138383898,2	K562	blood:

Variant related genes	Relation type
PIK3CB	TF binding region
ENSG00000114107	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1066197	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1068104	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1068685	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804658	1.00[CHB][hapmap]
rs1091528	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11706016	0.85[CEU][hapmap]
rs11708762	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs11720178	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12631035	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs12633714	0.89[CEU][hapmap]
rs13061496	0.85[CEU][hapmap]
rs13069296	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433948	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1663554	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1663556	0.85[EUR][1000 genomes]
rs1673597	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191713	0.81[EUR][1000 genomes]
rs191714	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs191775	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs244380	0.80[EUR][1000 genomes]
rs2595928	0.83[EUR][1000 genomes]
rs2595930	0.86[EUR][1000 genomes]
rs2607796	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376988	0.80[EUR][1000 genomes]
rs2881900	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361057	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361059	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs361060	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs361061	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs361062	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs361063	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs361064	0.83[AFR][1000 genomes]
rs361066	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361067	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361071	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs361072	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs361073	1.00[CHB][hapmap]
rs361074	1.00[CHB][hapmap]
rs361075	1.00[CHB][hapmap]
rs361076	1.00[CHB][hapmap]
rs361077	1.00[CHB][hapmap]
rs361079	0.80[AFR][1000 genomes]
rs361080	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs361081	0.82[EUR][1000 genomes]
rs361082	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs361083	0.81[EUR][1000 genomes]
rs361084	0.81[EUR][1000 genomes]
rs361088	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs361089	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361092	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361094	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs361096	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361097	0.84[EUR][1000 genomes]
rs385254	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs413147	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4305444	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs439720	0.81[EUR][1000 genomes]
rs470359	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475254	0.85[EUR][1000 genomes]
rs484698	1.00[CHB][hapmap]
rs4894359	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs493152	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs497900	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs500687	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs520904	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs523975	1.00[CHB][hapmap]
rs524164	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs531577	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs537894	1.00[CHB][hapmap]
rs550768	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558905	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs559160	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564455	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs589986	0.84[EUR][1000 genomes]
rs600590	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs601032	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs603723	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618457	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621204	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624099	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs625468	0.85[EUR][1000 genomes]
rs635592	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643620	1.00[CHB][hapmap]
rs6439817	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6773514	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs6784610	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7613579	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs7641106	0.89[ASN][1000 genomes]
rs7643722	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7650967	0.88[CEU][hapmap]
rs773045	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773184	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811322	1.00[CHB][hapmap]
rs9289566	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs9647336	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9647337	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9821694	0.92[CEU][hapmap]
rs9822714	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9834963	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9864176	0.85[EUR][1000 genomes]
rs9879784	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs361087	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs361087	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs361087	FAIM	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138340400-138393800	Weak transcription	Fetal Brain Male	brain
2	chr3:138360800-138407600	Weak transcription	HUVEC	blood vessel
3	chr3:138364400-138459200	Weak transcription	Psoas Muscle	Psoas
4	chr3:138368800-138386600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:138368800-138392400	Weak transcription	HMEC	breast
6	chr3:138368800-138400200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:138368800-138422600	Weak transcription	Right Atrium	heart
8	chr3:138369000-138390000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:138369000-138392400	Weak transcription	HSMM	muscle
10	chr3:138369000-138493000	Weak transcription	Fetal Lung	lung
11	chr3:138369200-138384800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:138369200-138391800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:138369200-138393600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:138369200-138401600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:138369200-138412800	Weak transcription	Hela-S3	cervix
16	chr3:138369200-138428800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:138369200-138435600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:138369400-138387000	Weak transcription	Pancreas	Pancrea
19	chr3:138369400-138392600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:138373000-138385800	Weak transcription	NHLF	lung
21	chr3:138373000-138390400	Weak transcription	NH-A	brain
22	chr3:138374200-138390600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:138374400-138389400	Weak transcription	Fetal Heart	heart
24	chr3:138374800-138392200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:138374800-138397000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:138375200-138429000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:138377000-138392800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:138377000-138394200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:138377400-138390400	Weak transcription	Right Ventricle	heart
30	chr3:138381800-138385800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:138381800-138385800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:138381800-138385800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:138381800-138389400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:138381800-138391200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:138381800-138394200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:138382000-138383600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:138382000-138383800	Strong transcription	Primary T cells from cord blood	blood
38	chr3:138382000-138384000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:138382000-138384000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:138382000-138384000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:138382000-138384000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:138382000-138384000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:138382000-138384000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:138382000-138384000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:138382000-138384200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:138382000-138384400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:138382000-138385200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr3:138382000-138385200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr3:138382000-138385400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:138382000-138385600	Strong transcription	Rectal Mucosa Donor 31	rectum

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