Variant report

Variant	rs2909212
Chromosome Location	chr17:66458006-66458007
allele	A/G
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	ZNF143	chr17:66457984-66458124	GM12878	blood:	n/a	n/a
2	GATA2	chr17:66457837-66458174	SH-SY5Y	brain:	n/a	n/a
3	SMC3	chr17:66457592-66460409	SK-N-SH	brain:	n/a	chr17:66459301-66459315
4	POLR2A	chr17:66457815-66458100	GM12878	blood:	n/a	n/a
5	TCF12	chr17:66457938-66458210	GM12878	blood:	n/a	n/a
6	MYC	chr17:66456870-66458297	K562	blood:	n/a	chr17:66457603-66457612
7	WRNIP1	chr17:66457553-66458226	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:66456274-66458213	GM12878	blood:	n/a	n/a
9	BHLHE40	chr17:66457883-66458121	K562	blood:	n/a	n/a
10	PML	chr17:66456235-66458224	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr17:66457380-66458191	K562	blood:	n/a	n/a
12	YY1	chr17:66457764-66458177	GM12878	blood:	n/a	n/a
13	EP300	chr17:66457428-66458223	GM12878	blood:	n/a	chr17:66457764-66457778 chr17:66457581-66457595
14	POLR2A	chr17:66457449-66458170	GM12892	blood:	n/a	n/a
15	STAT3	chr17:66457811-66458210	MCF10A-Er-Src	breast:	n/a	chr17:66457992-66458003 chr17:66457892-66457904 chr17:66457994-66458002 chr17:66457988-66458008 chr17:66457988-66458008
16	TCF3	chr17:66457808-66458159	GM12878	blood:	n/a	n/a
17	EBF1	chr17:66457737-66458149	GM12878	blood:	n/a	n/a
18	JUN	chr17:66456912-66458397	K562	blood:	n/a	n/a
19	NFYB	chr17:66457746-66458187	GM12878	blood:	n/a	chr17:66458016-66458029
20	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
21	MAZ	chr17:66457804-66458136	K562	blood:	n/a	n/a
22	JUND	chr17:66457005-66458206	K562	blood:	n/a	n/a
23	POLR2A	chr17:66457431-66458117	GM12878	blood:	n/a	n/a
24	RCOR1	chr17:66457064-66458203	K562	blood:	n/a	n/a
25	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
26	RUNX3	chr17:66457868-66458231	GM12878	blood:	n/a	n/a
27	TCF12	chr17:66457862-66458183	GM12878	blood:	n/a	n/a
28	FOS	chr17:66457443-66458050	MCF10A-Er-Src	breast:	n/a	n/a
29	RUNX3	chr17:66457482-66458239	GM12878	blood:	n/a	n/a
30	STAT3	chr17:66457818-66458151	MCF10A-Er-Src	breast:	n/a	chr17:66457992-66458003 chr17:66457892-66457904 chr17:66457994-66458002 chr17:66457988-66458008 chr17:66457988-66458008
31	EP300	chr17:66457040-66458213	K562	blood:	n/a	chr17:66457336-66457346 chr17:66457284-66457298 chr17:66457764-66457778 chr17:66457581-66457595
32	ATF1	chr17:66457457-66458045	K562	blood:	n/a	n/a
33	STAT1	chr17:66457841-66458068	GM12878	blood:	n/a	chr17:66457892-66457904 chr17:66457994-66458002 chr17:66457988-66458008 chr17:66457988-66458008 chr17:66457992-66458003
34	NFIC	chr17:66456658-66458271	GM12878	blood:	n/a	n/a
35	FOS	chr17:66457872-66458085	MCF10A-Er-Src	breast:	n/a	n/a
36	EBF1	chr17:66457631-66458219	GM12878	blood:	n/a	n/a
37	CUX1	chr17:66457232-66458184	K562	blood:	n/a	n/a
38	FOXM1	chr17:66457430-66458280	GM12878	blood:	n/a	n/a
39	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
40	MTA3	chr17:66457355-66458306	GM12878	blood:	n/a	n/a
41	STAT1	chr17:66457775-66458190	Hela-S3	cervix:	n/a	chr17:66457892-66457904 chr17:66457994-66458002 chr17:66457988-66458008 chr17:66457988-66458008 chr17:66457992-66458003
42	POLR2A	chr17:66457781-66458100	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	chr17:66457871..66459723-chr17:66755442..66757675,2	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
ENSG00000108946	Chromatin interaction
ENSG00000141337	Chromatin interaction
ENSG00000070540	Chromatin interaction
ENSG00000108932	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11656906	0.80[AFR][1000 genomes]
rs1808333	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2287301	0.80[AFR][1000 genomes]
rs2302782	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2909214	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2952291	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71378929	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs869657	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs918167	0.81[AFR][1000 genomes];0.81[AMR][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

No data

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	chr17:66454400-66458400	Weak transcription	Gastric	stomach
3	chr17:66454400-66458800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:66454400-66458800	Weak transcription	Lung	lung
5	chr17:66454600-66458800	Weak transcription	Pancreas	Pancrea
6	chr17:66454600-66459200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:66454600-66459400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr17:66454600-66459400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr17:66454600-66459400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr17:66454600-66459400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr17:66454600-66459400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr17:66454600-66464000	Weak transcription	Aorta	Aorta
13	chr17:66454600-66465200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:66454600-66470400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:66454800-66458600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:66454800-66458800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr17:66454800-66458800	Weak transcription	Brain Angular Gyrus	brain
18	chr17:66454800-66458800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr17:66454800-66459000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr17:66454800-66459000	Weak transcription	Brain Anterior Caudate	brain
21	chr17:66454800-66459000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr17:66454800-66459000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr17:66454800-66459000	Weak transcription	Colon Smooth Muscle	Colon
24	chr17:66454800-66459000	Weak transcription	Fetal Kidney	kidney
25	chr17:66454800-66459000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr17:66454800-66459000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr17:66454800-66459000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr17:66454800-66459400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr17:66454800-66462000	Weak transcription	Small Intestine	intestine
30	chr17:66454800-66462200	Weak transcription	Placenta	Placenta
31	chr17:66454800-66463600	Weak transcription	Right Atrium	heart
32	chr17:66455000-66458800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr17:66455000-66458800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr17:66455000-66459000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr17:66455000-66459600	Enhancers	K562	blood
36	chr17:66455400-66459200	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr17:66455600-66458600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr17:66455600-66458800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:66455600-66459400	Enhancers	Primary T cells from cord blood	blood
40	chr17:66456000-66459200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr17:66456000-66459400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr17:66456000-66459400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr17:66456000-66459400	Enhancers	Fetal Thymus	thymus
44	chr17:66456200-66458600	Weak transcription	Colonic Mucosa	Colon
45	chr17:66456200-66459200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr17:66456200-66459200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr17:66456200-66459200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr17:66456400-66458200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr17:66456400-66458200	Flanking Active TSS	GM12878-XiMat	blood
50	chr17:66456400-66459000	Enhancers	Thymus	Thymus

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