Variant report

Variant	rs9855727
Chromosome Location	chr3:138554852-138554853
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:138554537-138555139	K562	blood:	n/a	n/a
2	POLR2A	chr3:138554679-138554926	K562	blood:	n/a	n/a
3	POLR2A	chr3:138552926-138555297	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:138554696-138554853	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:138553797..138555960-chr3:138598138..138600170,2	K562	blood:
2	chr3:138552568..138555141-chr3:138666105..138668600,2	K562	blood:
3	chr3:138552259..138555153-chr3:138660631..138662853,2	K562	blood:
4	chr3:138552263..138555163-chr3:138665790..138667540,3	K562	blood:
5	chr3:138326713..138328588-chr3:138552751..138555574,2	MCF-7	breast:
6	chr3:138433313..138434820-chr3:138553042..138555465,2	MCF-7	breast:

No data

Variant related genes	Relation type
PIK3CB	TF binding region
ENSG00000206262	Chromatin interaction
ENSG00000183770	Chromatin interaction
ENSG00000158234	Chromatin interaction
ENSG00000051382	Chromatin interaction
ENSG00000244578	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10804659	0.92[EUR][1000 genomes]
rs10935288	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11705762	0.81[EUR][1000 genomes]
rs11706016	0.87[EUR][1000 genomes]
rs11708762	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11711360	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11713049	0.80[EUR][1000 genomes]
rs11720178	0.86[EUR][1000 genomes]
rs11924479	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11924814	0.80[EUR][1000 genomes]
rs12497815	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12631035	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12633714	0.89[EUR][1000 genomes]
rs12635713	0.81[EUR][1000 genomes]
rs13061496	0.87[EUR][1000 genomes]
rs13072146	0.84[EUR][1000 genomes]
rs13077455	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13082808	0.81[EUR][1000 genomes]
rs13100110	0.81[EUR][1000 genomes]
rs1400266	0.80[EUR][1000 genomes]
rs17484361	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28408150	0.81[EUR][1000 genomes]
rs2881900	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35214574	0.81[EUR][1000 genomes]
rs371762	0.81[EUR][1000 genomes]
rs413147	0.80[EUR][1000 genomes]
rs4405948	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4894358	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4894359	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62282169	0.80[EUR][1000 genomes]
rs62282204	0.80[EUR][1000 genomes]
rs6773514	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6776585	0.81[EUR][1000 genomes]
rs6780989	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6784610	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6791627	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6794270	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6800801	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6801207	0.80[EUR][1000 genomes]
rs6810351	0.81[EUR][1000 genomes]
rs7612106	0.81[EUR][1000 genomes]
rs7613579	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7628172	0.91[EUR][1000 genomes]
rs7646689	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7650967	0.92[EUR][1000 genomes]
rs9289566	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9647336	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9647337	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9813576	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9817727	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9818354	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9822500	0.89[EUR][1000 genomes]
rs9834963	0.80[EUR][1000 genomes]
rs9851887	0.84[EUR][1000 genomes]
rs9877108	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9879784	0.86[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
rs9855727	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs9855727	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138553000-138555000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:138554200-138555000	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr3:138554400-138555000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:138554400-138555000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:138554400-138555200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:138554400-138555200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:138554400-138555200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr3:138554400-138555200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:138554400-138555200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:138554400-138555200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:138554400-138555200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:138554400-138555200	Enhancers	Pancreas	Pancrea
13	chr3:138554400-138561400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:138554400-138561400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:138554600-138555000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr3:138554600-138555000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:138554600-138555000	Enhancers	Brain Anterior Caudate	brain
18	chr3:138554600-138555000	Enhancers	Fetal Brain Male	brain
19	chr3:138554600-138555000	Enhancers	Fetal Muscle Trunk	muscle
20	chr3:138554600-138555000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:138554600-138555200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:138554600-138555200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr3:138554600-138555200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:138554600-138555200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:138554600-138555200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:138554600-138555200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:138554600-138555200	Enhancers	Fetal Heart	heart
28	chr3:138554600-138555200	Enhancers	A549	lung
29	chr3:138554600-138555200	Enhancers	Dnd41	blood
30	chr3:138554600-138555200	Enhancers	Hela-S3	cervix
31	chr3:138554600-138555200	Enhancers	HepG2	liver
32	chr3:138554600-138555200	Enhancers	K562	blood

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