Variant report

Variant	rs72847784
Chromosome Location	chr17:66509702-66509703
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	TCF7L2	chr17:66509189-66510763	HEK293	kidney:	n/a	n/a
2	POLR2A	chr17:66507642-66510297	HUVEC	blood vessel:	n/a	n/a
3	TCF12	chr17:66507521-66509758	A549	lung:	n/a	chr17:66508919-66508929
4	POLR2A	chr17:66507543-66510391	MCF10A-Er-Src	breast:	n/a	n/a
5	JUN	chr17:66509530-66509736	K562	blood:	n/a	n/a
6	MXI1	chr17:66506146-66510554	SK-N-SH	brain:	n/a	chr17:66508093-66508102 chr17:66508484-66508499 chr17:66508095-66508104
7	CHD1	chr17:66507161-66511463	IMR90	lung:	n/a	n/a
8	MXI1	chr17:66507307-66509876	GM12878	blood:	n/a	chr17:66508093-66508102 chr17:66508484-66508499 chr17:66508095-66508104
9	MXI1	chr17:66507120-66510871	IMR90	lung:	n/a	chr17:66508093-66508102 chr17:66508484-66508499 chr17:66508095-66508104
10	POLR2A	chr17:66507852-66509754	GM12878	blood:	n/a	n/a
11	POLR2A	chr17:66507604-66510448	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr17:66509652-66510053	HepG2	liver:	n/a	n/a
13	HCFC1	chr17:66507322-66510244	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr17:66506962-66511766	IMR90	lung:	n/a	n/a
15	CHD1	chr17:66508774-66510043	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr17:66507294-66509952	PBDE	blood:	n/a	n/a
17	POLR2A	chr17:66507531-66509836	HCT-116	colon:	n/a	n/a
18	PML	chr17:66507432-66509711	MCF-7	breast:	n/a	n/a
19	MAZ	chr17:66507665-66509923	K562	blood:	n/a	chr17:66508092-66508101 chr17:66508090-66508105 chr17:66508092-66508107 chr17:66508094-66508104
20	POLR2A	chr17:66507358-66509879	GM12891	blood:	n/a	n/a
21	HEY1	chr17:66507334-66509961	HepG2	liver:	n/a	chr17:66507956-66507971 chr17:66508914-66508929 chr17:66508827-66508842 chr17:66507950-66507965 chr17:66508925-66508940 chr17:66508522-66508531
22	SIN3AK20	chr17:66507257-66510385	MCF-7	breast:	n/a	n/a
23	POLR2A	chr17:66507452-66510352	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr17:66509643-66509880	ProgFib	skin:	n/a	n/a
25	STAT3	chr17:66509549-66509734	MCF10A-Er-Src	breast:	n/a	chr17:66509608-66509622 chr17:66509611-66509619 chr17:66509609-66509620
26	POLR2A	chr17:66507538-66509832	Hela-S3	cervix:	n/a	n/a
27	STAT3	chr17:66509422-66509723	MCF10A-Er-Src	breast:	n/a	chr17:66509608-66509622 chr17:66509611-66509619 chr17:66509609-66509620
28	YY1	chr17:66507211-66509746	SK-N-SH	brain:	n/a	chr17:66508761-66508780 chr17:66508668-66508677 chr17:66508767-66508775 chr17:66508915-66508926 chr17:66508763-66508779 chr17:66508666-66508680 chr17:66508756-66508778 chr17:66508640-66508649 chr17:66508671-66508680 chr17:66508053-66508064
29	POLR2A	chr17:66508178-66510376	K562	blood:	n/a	n/a
30	POLR2A	chr17:66509700-66509707	Hela-S3	cervix:	n/a	n/a
31	MAZ	chr17:66507296-66509806	IMR90	lung:	n/a	chr17:66508092-66508101 chr17:66508090-66508105 chr17:66508092-66508107 chr17:66508094-66508104
32	POLR2A	chr17:66507765-66509883	GM12878	blood:	n/a	n/a
33	TBL1XR1	chr17:66509498-66509729	K562	blood:	n/a	n/a
34	STAT3	chr17:66509476-66509738	MCF10A-Er-Src	breast:	n/a	chr17:66509608-66509622 chr17:66509611-66509619 chr17:66509609-66509620
35	SIN3A	chr17:66507504-66509792	H1-hESC	embryonic stem cell:	n/a	n/a
36	HDAC2	chr17:66507409-66509740	MCF-7	breast:	n/a	chr17:66507529-66507543 chr17:66507528-66507542 chr17:66507781-66507800 chr17:66507501-66507515 chr17:66509507-66509516
37	REST	chr17:66507156-66509715	H1-neurons	neurons:	n/a	chr17:66507794-66507804 chr17:66507952-66507965 chr17:66507911-66507924 chr17:66507781-66507799 chr17:66507601-66507610 chr17:66507969-66507989

No.	Distal block	Cell Line	Cell type
1	chr17:65820674..65823268-chr17:66508486..66510670,2	MCF-7	breast:
2	chr17:66507304..66510193-chr5:1344921..1346652,2	MCF-7	breast:
3	chr17:66031856..66033575-chr17:66508155..66509939,2	MCF-7	breast:
4	chr17:66287636..66289963-chr17:66508320..66510109,2	K562	blood:
5	chr17:66507070..66510931-chr17:66511371..66513422,6	K562	blood:
6	chr17:66507858..66510140-chr17:66521050..66524441,3	K562	blood:
7	chr17:66451996..66456192-chr17:66506725..66511948,5	MCF-7	breast:
8	chr17:66452513..66457853-chr17:66506674..66510981,7	MCF-7	breast:
9	chr17:66509250..66511874-chr17:66538190..66540879,2	MCF-7	breast:

Variant related genes	Relation type
PRKAR1A	TF binding region
ENSG00000049656	Chromatin interaction
ENSG00000070540	Chromatin interaction
ENSG00000182481	Chromatin interaction
ENSG00000141337	Chromatin interaction
ENSG00000108950	Chromatin interaction
ENSG00000171634	Chromatin interaction
ENSG00000269657	Chromatin interaction
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10468444	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10491176	0.99[EUR][1000 genomes]
rs16972996	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16973034	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015212	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302235	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785905	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55736761	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56112060	0.83[ASN][1000 genomes]
rs7221724	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847781	0.86[ASN][1000 genomes]
rs72847782	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72847785	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847787	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72847789	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847790	0.99[EUR][1000 genomes]
rs72847794	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847801	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74000753	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8067357	0.83[ASN][1000 genomes]
rs8072598	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8082254	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66507200-66510400	Active TSS	H1 Cell Line	embryonic stem cell
2	chr17:66507200-66510400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr17:66507200-66510800	Active TSS	GM12878-XiMat	blood
4	chr17:66507200-66511400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr17:66507400-66509800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:66507400-66509800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr17:66507400-66509800	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr17:66507400-66510000	Active TSS	Brain Substantia Nigra	brain
9	chr17:66507400-66510200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr17:66507400-66510200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr17:66507400-66510200	Active TSS	Brain Cingulate Gyrus	brain
12	chr17:66507400-66510400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr17:66507400-66510400	Active TSS	Muscle Satellite Cultured Cells	--
14	chr17:66507400-66510600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:66507400-66510600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr17:66507400-66511000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr17:66507400-66511000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr17:66507400-66511000	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr17:66507400-66511400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr17:66507400-66513600	Active TSS	Right Ventricle	heart
21	chr17:66507600-66509800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:66507600-66509800	Active TSS	Brain Angular Gyrus	brain
23	chr17:66507600-66509800	Active TSS	Brain Hippocampus Middle	brain
24	chr17:66507600-66510000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr17:66507600-66510000	Active TSS	Fetal Brain Female	brain
26	chr17:66507600-66510000	Bivalent/Poised TSS	HepG2	liver
27	chr17:66507600-66510200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr17:66507600-66510200	Active TSS	Fetal Kidney	kidney
29	chr17:66507600-66510400	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr17:66507600-66510400	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr17:66507600-66510400	Active TSS	Fetal Intestine Large	intestine
32	chr17:66507600-66510400	Active TSS	Hela-S3	cervix
33	chr17:66507600-66510600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr17:66507600-66510800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:66507600-66510800	Active TSS	NHDF-Ad	bronchial
36	chr17:66507600-66511000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr17:66507600-66511200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr17:66507600-66511200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr17:66507600-66511200	Active TSS	Left Ventricle	heart
40	chr17:66507600-66511400	Active TSS	Aorta	Aorta
41	chr17:66507600-66511600	Active TSS	Ovary	ovary
42	chr17:66507800-66509800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr17:66507800-66509800	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr17:66507800-66509800	Active TSS	Brain Anterior Caudate	brain
45	chr17:66507800-66509800	Active TSS	Colon Smooth Muscle	Colon
46	chr17:66507800-66509800	Active TSS	Placenta Amnion	Placenta Amnion
47	chr17:66507800-66509800	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr17:66507800-66509800	Active TSS	Small Intestine	intestine
49	chr17:66507800-66510000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr17:66507800-66510000	Active TSS	Duodenum Mucosa	Duodenum

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