Variant report

Variant	rs8080306
Chromosome Location	chr17:66508243-66508244
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	chr17:66507361-66509610	HepG2	liver:	n/a	n/a
2	EGR1	chr17:66507342-66509645	MCF-7	breast:	n/a	chr17:66508937-66508951 chr17:66508111-66508125 chr17:66508940-66508953 chr17:66508940-66508950 chr17:66508858-66508868
3	POLR2A	chr17:66507671-66509455	GM12892	blood:	n/a	n/a
4	SMC3	chr17:66508160-66508433	HepG2	liver:	n/a	n/a
5	MAX	chr17:66507652-66509481	A549	lung:	n/a	chr17:66508092-66508101 chr17:66508090-66508105 chr17:66508092-66508107 chr17:66508094-66508104
6	TBL1XR1	chr17:66508111-66508631	K562	blood:	n/a	n/a
7	POLR2A	chr17:66507586-66509547	GM18505	blood:	n/a	n/a
8	ELF1	chr17:66508117-66508781	K562	blood:	n/a	chr17:66508640-66508649 chr17:66508667-66508679 chr17:66508671-66508680
9	MAX	chr17:66507931-66509540	NB4	blood:	n/a	chr17:66508092-66508101 chr17:66508090-66508105 chr17:66508092-66508107 chr17:66508094-66508104
10	SPI1	chr17:66508171-66508954	GM12878	blood:	n/a	chr17:66508812-66508825 chr17:66508451-66508464
11	RUNX3	chr17:66507617-66509062	GM12878	blood:	n/a	n/a
12	USF1	chr17:66507810-66508393	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr17:66507747-66509486	GM12891	blood:	n/a	n/a
14	MXI1	chr17:66507451-66509205	HepG2	liver:	n/a	chr17:66508093-66508102 chr17:66508484-66508499 chr17:66508095-66508104
15	POLR2A	chr17:66507653-66509133	Gliobla	brain:	n/a	n/a
16	CHD2	chr17:66507695-66509597	Hela-S3	cervix:	n/a	n/a
17	SIN3AK20	chr17:66507447-66509605	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F6	chr17:66507695-66509011	Hela-S3	cervix:	n/a	chr17:66508542-66508551 chr17:66508124-66508135 chr17:66507997-66508007 chr17:66508669-66508679 chr17:66508195-66508206 chr17:66508668-66508677 chr17:66508919-66508929 chr17:66508522-66508531
19	RCOR1	chr17:66507530-66509123	K562	blood:	n/a	n/a
20	CREB1	chr17:66508151-66509015	K562	blood:	n/a	n/a
21	TCF7L2	chr17:66507935-66508622	MCF-7	breast:	n/a	chr17:66508246-66508256
22	TBP	chr17:66508069-66508917	K562	blood:	n/a	n/a
23	TBP	chr17:66507726-66509596	H1-hESC	embryonic stem cell:	n/a	n/a
24	ELK4	chr17:66508013-66508929	Hela-S3	cervix:	n/a	chr17:66508559-66508570 chr17:66508561-66508570
25	NFIC	chr17:66508200-66508885	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr17:66507642-66510297	HUVEC	blood vessel:	n/a	n/a
27	CREB1	chr17:66508034-66508956	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr17:66507630-66509614	GM12878	blood:	n/a	n/a
29	SP1	chr17:66507839-66509345	A549	lung:	n/a	chr17:66508451-66508462 chr17:66508531-66508552 chr17:66508811-66508825 chr17:66508817-66508826 chr17:66508816-66508825
30	EGR1	chr17:66507730-66509385	HCT-116	colon:	n/a	chr17:66508937-66508951 chr17:66508111-66508125 chr17:66508940-66508953 chr17:66508940-66508950 chr17:66508858-66508868
31	HCFC1	chr17:66507704-66509330	K562	blood:	n/a	n/a
32	RCOR1	chr17:66507879-66508571	K562	blood:	n/a	n/a
33	TCF12	chr17:66507521-66509758	A549	lung:	n/a	chr17:66508919-66508929
34	SMC3	chr17:66507655-66509478	Hela-S3	cervix:	n/a	chr17:66508448-66508458
35	POLR2A	chr17:66507543-66510391	MCF10A-Er-Src	breast:	n/a	n/a
36	RFX5	chr17:66507718-66508722	HepG2	liver:	n/a	chr17:66508482-66508499 chr17:66508483-66508498 chr17:66508483-66508498 chr17:66508541-66508550 chr17:66508481-66508495 chr17:66508483-66508498 chr17:66508484-66508493
37	MAX	chr17:66507801-66508927	ECC-1	luminal epithelium:	n/a	chr17:66508092-66508101 chr17:66508090-66508105 chr17:66508092-66508107 chr17:66508094-66508104
38	GTF2F1	chr17:66507646-66508841	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr17:66507644-66509650	GM12878	blood:	n/a	n/a
40	MBD4	chr17:66507931-66508631	HepG2	liver:	n/a	n/a
41	POLR2A	chr17:66507822-66508273	A549	lung:	n/a	n/a
42	E2F6	chr17:66507628-66509195	K562	blood:	n/a	chr17:66508542-66508551 chr17:66508124-66508135 chr17:66507997-66508007 chr17:66508669-66508679 chr17:66508195-66508206 chr17:66508668-66508677 chr17:66508919-66508929 chr17:66508522-66508531
43	POLR2A	chr17:66507335-66508846	HepG2	liver:	n/a	n/a
44	SP1	chr17:66507795-66509615	A549	lung:	n/a	chr17:66508451-66508462 chr17:66508531-66508552 chr17:66508811-66508825 chr17:66508817-66508826 chr17:66508816-66508825
45	CHD2	chr17:66508081-66509153	HepG2	liver:	n/a	n/a
46	POLR2A	chr17:66507750-66509241	GM18526	blood:	n/a	n/a
47	USF1	chr17:66507849-66508707	A549	lung:	n/a	chr17:66508670-66508686
48	GABPA	chr17:66507683-66509034	MCF-7	breast:	n/a	n/a
49	CREB1	chr17:66507756-66508318	A549	lung:	n/a	n/a
50	RAD21	chr17:66507584-66508405	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:66508232-66508282	HEEpiC	esophagus:	n/a
2	chr17:66508232-66508282	HUVEC	blood vessel:	n/a
3	chr17:66508232-66508282	RPTEC	kidney:	n/a
4	chr17:66508232-66508282	Caco-2	colon:	n/a
5	chr17:66508232-66508282	GM19239	blood:	n/a
6	chr17:66508232-66508282	A549	lung:	n/a
7	chr17:66508232-66508282	HPAEpiC	pulmonary alveolar:	n/a
8	chr17:66508232-66508282	T-47D	breast:	n/a
9	chr17:66508232-66508282	NT2-D1	testis:	n/a
10	chr17:66508232-66508282	AG04449	skin:	fetal
11	chr17:66508232-66508282	AoSMC	blood vessel:	n/a
12	chr17:66508232-66508282	HRPEpiC	eye:	n/a
13	chr17:66508232-66508282	SKMC	muscle:	n/a
14	chr17:66508232-66508282	Hela-S3	cervix:	n/a
15	chr17:66508232-66508282	AG04450	lung:	fetal
16	chr17:66508232-66508282	HIPEpiC	eye:	n/a
17	chr17:66508232-66508282	PANC-1	pancreas:	n/a
18	chr17:66508232-66508282	BE2_C	brain:	n/a
19	chr17:66508232-66508282	GM06990	blood:	n/a
20	chr17:66508232-66508282	NHBE	bronchial:	n/a
21	chr17:66508232-66508282	NB4	blood:	n/a
22	chr17:66508232-66508282	PFSK-1	brain:	n/a
23	chr17:66508232-66508282	K562	blood:	n/a
24	chr17:66508232-66508282	Hepatocyte	liver:	n/a
25	chr17:66508232-66508282	SK-N-SH	brain:	n/a
26	chr17:66508232-66508282	HL-60	blood:	n/a
27	chr17:66508232-66508282	MCF-7	breast:	n/a
28	chr17:66508232-66508282	U87	brain:	n/a
29	chr17:66508232-66508282	ECC-1	luminal epithelium:	n/a
30	chr17:66508232-66508282	HCM	heart:	n/a
31	chr17:66508232-66508282	HMEC	breast:	n/a
32	chr17:66508232-66508282	MCF10A-Er-Src	breast:	n/a
33	chr17:66508232-66508282	AG09319	gingival:	n/a
34	chr17:66508232-66508282	ovcar-3	ovarian:	n/a
35	chr17:66508232-66508282	SK-N-MC	brain:	n/a
36	chr17:66508232-66508282	HAEpiC	amniotic membrane:	n/a
37	chr17:66508232-66508282	AG10803	skin:	n/a
38	chr17:66508232-66508282	IMR90	lung:	fetal
39	chr17:66508232-66508282	BJ	skin:	n/a
40	chr17:66508232-66508282	HCT-116	colon:	n/a
41	chr17:66508232-66508282	SK-N-SH_RA	brain:	n/a
42	chr17:66508232-66508282	HEK293	kidney:	embryo
43	chr17:66508232-66508282	SAEC	small airway:	n/a
44	chr17:66508232-66508282	HepG2	liver:	n/a
45	chr17:66508232-66508282	GM12891	blood:	n/a
46	chr17:66508232-66508282	LNCaP	prostate:	n/a
47	chr17:66508232-66508282	AG09309	skin:	n/a
48	chr17:66508232-66508282	GM12878	blood:	n/a
49	chr17:66508232-66508282	HCPEpiC	choroid plexus:	n/a
50	chr17:66508232-66508282	H1-hESC	embryonic stem cell:	embryo

No.	Distal block	Cell Line	Cell type
1	chr17:66507304..66510193-chr5:1344921..1346652,2	MCF-7	breast:
2	chr1:78148215..78149119-chr17:66507710..66508529,2	Hela-S3	cervix:
3	chr17:66286763..66288590-chr17:66507383..66509365,2	MCF-7	breast:
4	chr17:66031856..66033575-chr17:66508155..66509939,2	MCF-7	breast:
5	chr17:66507070..66510931-chr17:66511371..66513422,6	K562	blood:
6	chr17:57922676..57925665-chr17:66507184..66508973,2	MCF-7	breast:
7	chr17:66507858..66510140-chr17:66521050..66524441,3	K562	blood:
8	chr15:65596682..65597478-chr17:66507491..66508484,2	Hela-S3	cervix:
9	chr17:66242526..66245524-chr17:66505598..66508247,2	MCF-7	breast:
10	chr17:66451996..66456192-chr17:66506725..66511948,5	MCF-7	breast:
11	chr17:65988026..65990117-chr17:66506975..66509673,3	K562	blood:
12	chr17:66452513..66457853-chr17:66506674..66510981,7	MCF-7	breast:
13	chr17:66506755..66509358-chr17:66521590..66523476,3	K562	blood:

Variant related genes	Relation type
PRKAR1A	TF binding region
PRKAR1A	CpG island
ENSG00000196704	Chromatin interaction
ENSG00000070540	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000182481	Chromatin interaction
ENSG00000049656	Chromatin interaction
ENSG00000108932	Chromatin interaction
ENSG00000265100	Chromatin interaction
ENSG00000141337	Chromatin interaction
ENSG00000108946	Chromatin interaction
ENSG00000036549	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000186665	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2286559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2952278	1.00[CHB][hapmap]
rs4321253	0.80[EUR][1000 genomes]
rs6501512	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs7207491	0.82[EUR][1000 genomes]
rs7222188	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs8066131	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs8069982	0.86[CEU][hapmap]
rs9894682	0.82[EUR][1000 genomes]
rs9898700	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
2	esv3409910	chr17:66507582-66510130	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8080306	CD79B	cis	cerebellum	SCAN
rs8080306	WIPI1	cis	parietal	SCAN
rs8080306	PRKAR1A	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66507200-66508400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:66507200-66510400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr17:66507200-66510400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr17:66507200-66510800	Active TSS	GM12878-XiMat	blood
5	chr17:66507200-66511400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr17:66507400-66508400	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr17:66507400-66508400	Flanking Active TSS	Liver	Liver
8	chr17:66507400-66508400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr17:66507400-66508600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:66507400-66508600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr17:66507400-66508600	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr17:66507400-66509200	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr17:66507400-66509800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:66507400-66509800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr17:66507400-66509800	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr17:66507400-66510000	Active TSS	Brain Substantia Nigra	brain
17	chr17:66507400-66510200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr17:66507400-66510200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr17:66507400-66510200	Active TSS	Brain Cingulate Gyrus	brain
20	chr17:66507400-66510400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr17:66507400-66510400	Active TSS	Muscle Satellite Cultured Cells	--
22	chr17:66507400-66510600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:66507400-66510600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:66507400-66511000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:66507400-66511000	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr17:66507400-66511000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr17:66507400-66511400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:66507400-66513600	Active TSS	Right Ventricle	heart
29	chr17:66507600-66508400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr17:66507600-66508400	Flanking Active TSS	Dnd41	blood
31	chr17:66507600-66508400	Flanking Active TSS	HUVEC	blood vessel
32	chr17:66507600-66509400	Active TSS	Primary T cells from cord blood	blood
33	chr17:66507600-66509400	Active TSS	Fetal Brain Male	brain
34	chr17:66507600-66509600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:66507600-66509600	Active TSS	Gastric	stomach
36	chr17:66507600-66509600	Active TSS	Lung	lung
37	chr17:66507600-66509800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:66507600-66509800	Active TSS	Brain Angular Gyrus	brain
39	chr17:66507600-66509800	Active TSS	Brain Hippocampus Middle	brain
40	chr17:66507600-66510000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr17:66507600-66510000	Active TSS	Fetal Brain Female	brain
42	chr17:66507600-66510000	Bivalent/Poised TSS	HepG2	liver
43	chr17:66507600-66510200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr17:66507600-66510200	Active TSS	Fetal Kidney	kidney
45	chr17:66507600-66510400	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr17:66507600-66510400	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr17:66507600-66510400	Active TSS	Fetal Intestine Large	intestine
48	chr17:66507600-66510400	Active TSS	Hela-S3	cervix
49	chr17:66507600-66510600	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr17:66507600-66510800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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