Variant report

Variant	rs333992
Chromosome Location	chr2:179144980-179144981
allele	C/T
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	RAD21	chr2:179144955-179145445	ECC-1	luminal epithelium:	n/a	n/a
2	NFYB	chr2:179144936-179145312	Hela-S3	cervix:	n/a	chr2:179145122-179145137 chr2:179145123-179145133
3	RAD21	chr2:179144942-179145505	HCT-116	colon:	n/a	n/a
4	CTCF	chr2:179144977-179145311	H1-hESC	embryonic stem cell:	n/a	chr2:179145190-179145199
5	NFYB	chr2:179144924-179145310	GM12878	blood:	n/a	chr2:179145122-179145137 chr2:179145123-179145133
6	RAD21	chr2:179144951-179145339	SK-N-SH_RA	brain:	n/a	n/a
7	RAD21	chr2:179144826-179145478	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr2:179144900-179145050	GM12864	blood:	n/a	n/a
9	SMC3	chr2:179144925-179145511	SK-N-SH	brain:	n/a	n/a
10	NFYA	chr2:179144953-179145137	GM12878	blood:	n/a	chr2:179145123-179145133 chr2:179145116-179145134
11	RAD21	chr2:179144964-179145287	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr2:179144922-179145359	HepG2	liver:	n/a	n/a
13	RAD21	chr2:179144955-179145358	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr2:179144909-179145525	HCT-116	colon:	n/a	chr2:179145190-179145199
15	CTCF	chr2:179144894-179145546	A549	lung:	n/a	chr2:179145190-179145199
16	RAD21	chr2:179144933-179145352	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr2:179144957-179145467	MCF-7	breast:	n/a	n/a
18	CTCF	chr2:179144905-179145459	SK-N-SH	brain:	n/a	chr2:179145190-179145199
19	CBX3	chr2:179144961-179145437	HCT-116	colon:	n/a	n/a
20	CTCF	chr2:179144933-179145461	HCT-116	colon:	n/a	chr2:179145190-179145199
21	CTCF	chr2:179144919-179145447	MCF-7	breast:	n/a	chr2:179145190-179145199
22	RAD21	chr2:179144899-179145455	HCT-116	colon:	n/a	n/a
23	CTCF	chr2:179144900-179145050	A549	lung:	n/a	n/a
24	RAD21	chr2:179144960-179145345	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:178996751..178997649-chr2:179144316..179145071,2	MCF-7	breast:
2	chr2:178848052..178848705-chr2:179144772..179145465,2	K562	blood:
3	chr2:179058030..179060650-chr2:179143594..179145205,2	K562	blood:
4	chr2:179140566..179142281-chr2:179143545..179145094,2	K562	blood:

Variant related genes	Relation type
OSBPL6	TF binding region
ENSG00000079156	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs101266	0.94[JPT][hapmap]
rs12185670	0.81[JPT][hapmap]
rs12476671	0.93[JPT][hapmap]
rs1434080	0.83[JPT][hapmap]
rs147180	0.94[JPT][hapmap]
rs333993	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333994	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333997	0.94[JPT][hapmap]
rs334002	0.88[CEU][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs334009	0.93[JPT][hapmap]
rs334013	0.94[JPT][hapmap]
rs334014	0.94[JPT][hapmap]
rs334037	0.81[JPT][hapmap]
rs334604	0.85[CEU][hapmap]
rs334616	0.88[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs334620	0.82[JPT][hapmap]
rs334622	0.82[JPT][hapmap]
rs334623	0.89[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs334630	0.82[JPT][hapmap]
rs334631	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs551368	0.94[JPT][hapmap]
rs7587549	0.83[JPT][hapmap]
rs7592114	0.86[MEX][hapmap]
rs7599683	0.88[CEU][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs9989738	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs333992	OLA1	cis	cerebellum	SCAN
rs333992	FKBP7	cis	cerebellum	SCAN
rs333992	LOC100130691	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179133800-179146800	Weak transcription	Esophagus	oesophagus
2	chr2:179136800-179146800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:179141000-179146800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:179141200-179146800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:179141600-179145600	Enhancers	Fetal Intestine Small	intestine
6	chr2:179142400-179145000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:179142400-179145000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:179142400-179145200	Enhancers	Fetal Intestine Large	intestine
9	chr2:179142400-179145200	Enhancers	NHDF-Ad	bronchial
10	chr2:179142800-179145200	Enhancers	HUVEC	blood vessel
11	chr2:179142800-179146600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:179142800-179146800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:179142800-179146800	Weak transcription	Brain Angular Gyrus	brain
14	chr2:179143000-179145000	Enhancers	Liver	Liver
15	chr2:179143000-179145000	Enhancers	NH-A	brain
16	chr2:179143000-179146600	Weak transcription	A549	lung
17	chr2:179143000-179146800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:179143000-179146800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:179143000-179146800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:179143000-179160200	Weak transcription	Fetal Kidney	kidney
21	chr2:179143200-179160800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:179143200-179188600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:179143400-179146800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:179143600-179145400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:179143600-179146600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:179144000-179146800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:179144000-179148400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:179144200-179163800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:179144400-179145000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:179144400-179146800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:179144400-179153000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr2:179144400-179154600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:179144600-179145400	Enhancers	HMEC	breast
34	chr2:179144600-179146600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:179144600-179146600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:179144600-179146600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:179144600-179146600	Weak transcription	Hela-S3	cervix
38	chr2:179144600-179146600	Weak transcription	K562	blood
39	chr2:179144600-179146600	Weak transcription	Osteobl	bone
40	chr2:179144600-179146800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:179144600-179146800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:179144600-179146800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:179144600-179146800	Weak transcription	Psoas Muscle	Psoas
44	chr2:179144600-179147000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:179144600-179147000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:179144600-179149400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:179144600-179149600	Weak transcription	HSMMtube	muscle
48	chr2:179144600-179155000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:179144800-179146600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:179144800-179146600	Weak transcription	NHEK	skin

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