Variant report

Variant	rs2909211
Chromosome Location	chr17:66457658-66457659
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	SMC3	chr17:66457592-66460409	SK-N-SH	brain:	n/a	chr17:66459301-66459315
2	EP300	chr17:66457023-66457775	Hela-S3	cervix:	n/a	chr17:66457336-66457346 chr17:66457284-66457298 chr17:66457581-66457595
3	MYC	chr17:66456870-66458297	K562	blood:	n/a	chr17:66457603-66457612
4	WRNIP1	chr17:66457553-66458226	GM12878	blood:	n/a	n/a
5	POLR2A	chr17:66456274-66458213	GM12878	blood:	n/a	n/a
6	SRF	chr17:66457532-66457664	GM12878	blood:	n/a	n/a
7	PML	chr17:66456235-66458224	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr17:66457380-66458191	K562	blood:	n/a	n/a
9	EP300	chr17:66457428-66458223	GM12878	blood:	n/a	chr17:66457764-66457778 chr17:66457581-66457595
10	POLR2A	chr17:66457449-66458170	GM12892	blood:	n/a	n/a
11	ZKSCAN1	chr17:66457564-66457783	Hela-S3	cervix:	n/a	n/a
12	JUN	chr17:66456912-66458397	K562	blood:	n/a	n/a
13	MEF2C	chr17:66457627-66458316	GM12878	blood:	n/a	chr17:66457748-66457756 chr17:66458081-66458102 chr17:66458262-66458270 chr17:66458086-66458095 chr17:66458083-66458098 chr17:66458083-66458099 chr17:66458079-66458100 chr17:66458085-66458096
14	JUND	chr17:66457005-66458206	K562	blood:	n/a	n/a
15	POLR2A	chr17:66457431-66458117	GM12878	blood:	n/a	n/a
16	MAFK	chr17:66457260-66457661	K562	blood:	n/a	chr17:66457412-66457423 chr17:66457542-66457553 chr17:66457541-66457552 chr17:66457411-66457425 chr17:66457542-66457553 chr17:66457541-66457557 chr17:66457408-66457424 chr17:66457413-66457424 chr17:66457408-66457423 chr17:66457540-66457554 chr17:66457413-66457424 chr17:66457541-66457552
17	CEBPB	chr17:66457116-66457802	K562	blood:	n/a	chr17:66457461-66457473
18	RCOR1	chr17:66457064-66458203	K562	blood:	n/a	n/a
19	MAX	chr17:66457433-66457730	Hela-S3	cervix:	n/a	chr17:66457603-66457612
20	MAFK	chr17:66457078-66457704	Hela-S3	cervix:	n/a	chr17:66457412-66457423 chr17:66457542-66457553 chr17:66457541-66457552 chr17:66457411-66457425 chr17:66457542-66457553 chr17:66457541-66457557 chr17:66457408-66457424 chr17:66457413-66457424 chr17:66457408-66457423 chr17:66457540-66457554 chr17:66457413-66457424 chr17:66457541-66457552
21	MEF2A	chr17:66457572-66458322	GM12878	blood:	n/a	chr17:66457748-66457756 chr17:66458081-66458102 chr17:66458262-66458270 chr17:66458086-66458095 chr17:66458083-66458098 chr17:66458083-66458099 chr17:66458079-66458100 chr17:66458085-66458096
22	FOS	chr17:66457443-66458050	MCF10A-Er-Src	breast:	n/a	n/a
23	RUNX3	chr17:66457482-66458239	GM12878	blood:	n/a	n/a
24	EP300	chr17:66457040-66458213	K562	blood:	n/a	chr17:66457336-66457346 chr17:66457284-66457298 chr17:66457764-66457778 chr17:66457581-66457595
25	ATF1	chr17:66457457-66458045	K562	blood:	n/a	n/a
26	CEBPB	chr17:66457490-66457769	H1-hESC	embryonic stem cell:	n/a	n/a
27	NFIC	chr17:66456658-66458271	GM12878	blood:	n/a	n/a
28	CEBPB	chr17:66457016-66457876	Hela-S3	cervix:	n/a	chr17:66457461-66457473
29	EBF1	chr17:66457631-66458219	GM12878	blood:	n/a	n/a
30	CEBPB	chr17:66457443-66457744	K562	blood:	n/a	chr17:66457461-66457473
31	CEBPB	chr17:66457508-66457681	K562	blood:	n/a	n/a
32	FOS	chr17:66457453-66457988	MCF10A-Er-Src	breast:	n/a	n/a
33	CUX1	chr17:66457232-66458184	K562	blood:	n/a	n/a
34	FOXM1	chr17:66457430-66458280	GM12878	blood:	n/a	n/a
35	STAT3	chr17:66457553-66458151	MCF10A-Er-Src	breast:	n/a	chr17:66457992-66458003 chr17:66457892-66457904 chr17:66457994-66458002 chr17:66457988-66458008 chr17:66457988-66458008
36	TBP	chr17:66457472-66457802	Hela-S3	cervix:	n/a	n/a
37	MTA3	chr17:66457355-66458306	GM12878	blood:	n/a	n/a
38	STAT3	chr17:66456513-66457784	GM12878	blood:	n/a	chr17:66456730-66456737 chr17:66457366-66457380 chr17:66457002-66457013 chr17:66457303-66457311 chr17:66457004-66457012 chr17:66456998-66457018 chr17:66457001-66457015
39	MAX	chr17:66457513-66457729	K562	blood:	n/a	chr17:66457603-66457612
40	GTF2F1	chr17:66457429-66457780	Hela-S3	cervix:	n/a	n/a
41	TBP	chr17:66456384-66457692	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:66287633..66289379-chr17:66457483..66460091,3	K562	blood:
2	chr17:66428072..66429724-chr17:66457581..66460246,2	MCF-7	breast:
3	chr17:66456309..66458801-chr17:66507284..66509337,2	MCF-7	breast:
4	chr17:66259355..66259857-chr17:66457513..66458311,2	K562	blood:
5	chr17:66286556..66289379-chr17:66457092..66459088,2	K562	blood:
6	chr17:66456970..66458929-chr17:66509436..66511507,2	MCF-7	breast:
7	chr17:66452513..66457853-chr17:66506674..66510981,7	MCF-7	breast:
8	chr17:66241114..66243541-chr17:66457645..66460570,2	MCF-7	breast:
9	chr17:66436286..66439070-chr17:66455926..66458072,2	K562	blood:
10	chr17:66273184..66275331-chr17:66457154..66459234,2	MCF-7	breast:

Variant related genes	Relation type
WIPI1	TF binding region
ENSG00000070540	Chromatin interaction
ENSG00000108946	Chromatin interaction
ENSG00000108932	Chromatin interaction
ENSG00000141337	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11868680	0.87[ASN][1000 genomes]
rs1808335	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2111508	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302783	0.91[ASN][1000 genomes]
rs2909209	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2909213	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2909216	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2909217	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2909218	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2909220	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2909221	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2952277	0.81[EUR][1000 genomes]
rs2952279	0.81[EUR][1000 genomes]
rs2952284	0.84[EUR][1000 genomes]
rs2952286	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2952289	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2952290	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2952294	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2952295	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2952296	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71378928	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs883541	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2909211	PRKAR1A	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66453600-66462000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:66454400-66457800	Weak transcription	Esophagus	oesophagus
3	chr17:66454400-66458400	Weak transcription	Gastric	stomach
4	chr17:66454400-66458800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:66454400-66458800	Weak transcription	Lung	lung
6	chr17:66454600-66457800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr17:66454600-66458800	Weak transcription	Pancreas	Pancrea
8	chr17:66454600-66459200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:66454600-66459400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr17:66454600-66459400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:66454600-66459400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr17:66454600-66459400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr17:66454600-66459400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr17:66454600-66464000	Weak transcription	Aorta	Aorta
15	chr17:66454600-66465200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:66454600-66470400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:66454800-66457800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:66454800-66457800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr17:66454800-66458600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr17:66454800-66458800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr17:66454800-66458800	Weak transcription	Brain Angular Gyrus	brain
22	chr17:66454800-66458800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr17:66454800-66459000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr17:66454800-66459000	Weak transcription	Brain Anterior Caudate	brain
25	chr17:66454800-66459000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr17:66454800-66459000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr17:66454800-66459000	Weak transcription	Colon Smooth Muscle	Colon
28	chr17:66454800-66459000	Weak transcription	Fetal Kidney	kidney
29	chr17:66454800-66459000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr17:66454800-66459000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr17:66454800-66459000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr17:66454800-66459400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr17:66454800-66462000	Weak transcription	Small Intestine	intestine
34	chr17:66454800-66462200	Weak transcription	Placenta	Placenta
35	chr17:66454800-66463600	Weak transcription	Right Atrium	heart
36	chr17:66455000-66458800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr17:66455000-66458800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:66455000-66459000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr17:66455000-66459600	Enhancers	K562	blood
40	chr17:66455400-66459200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr17:66455600-66458600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr17:66455600-66458800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr17:66455600-66459400	Enhancers	Primary T cells from cord blood	blood
44	chr17:66455800-66457800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr17:66456000-66458000	Enhancers	Primary hematopoietic stem cells	blood
46	chr17:66456000-66459200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:66456000-66459400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr17:66456000-66459400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr17:66456000-66459400	Enhancers	Fetal Thymus	thymus
50	chr17:66456200-66458600	Weak transcription	Colonic Mucosa	Colon

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