Variant report

Variant	rs12941038
Chromosome Location	chr17:66509143-66509144
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	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	SIN3AK20	chr17:66508282-66509159	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr17:66507671-66509455	GM12892	blood:	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	POLR2A	chr17:66507586-66509547	GM18505	blood:	n/a	n/a
7	MAX	chr17:66507931-66509540	NB4	blood:	n/a	chr17:66508092-66508101 chr17:66508090-66508105 chr17:66508092-66508107 chr17:66508094-66508104
8	POLR2A	chr17:66507747-66509486	GM12891	blood:	n/a	n/a
9	MXI1	chr17:66507451-66509205	HepG2	liver:	n/a	chr17:66508093-66508102 chr17:66508484-66508499 chr17:66508095-66508104
10	KAP1	chr17:66509138-66509676	HEK293	kidney:	n/a	n/a
11	CHD2	chr17:66507695-66509597	Hela-S3	cervix:	n/a	n/a
12	SIN3AK20	chr17:66507447-66509605	H1-hESC	embryonic stem cell:	n/a	n/a
13	TBP	chr17:66507726-66509596	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr17:66507642-66510297	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr17:66507630-66509614	GM12878	blood:	n/a	n/a
16	SP1	chr17:66507839-66509345	A549	lung:	n/a	chr17:66508451-66508462 chr17:66508531-66508552 chr17:66508811-66508825 chr17:66508817-66508826 chr17:66508816-66508825
17	YY1	chr17:66508283-66509473	GM12891	blood:	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
18	POLR2A	chr17:66508946-66509194	K562	blood:	n/a	n/a
19	EGR1	chr17:66507730-66509385	HCT-116	colon:	n/a	chr17:66508937-66508951 chr17:66508111-66508125 chr17:66508940-66508953 chr17:66508940-66508950 chr17:66508858-66508868
20	EBF1	chr17:66509093-66509664	GM12878	blood:	n/a	chr17:66509472-66509483 chr17:66509472-66509485
21	HCFC1	chr17:66507704-66509330	K562	blood:	n/a	n/a
22	TCF12	chr17:66507521-66509758	A549	lung:	n/a	chr17:66508919-66508929
23	SMC3	chr17:66507655-66509478	Hela-S3	cervix:	n/a	chr17:66508448-66508458
24	POLR2A	chr17:66507543-66510391	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr17:66507644-66509650	GM12878	blood:	n/a	n/a
26	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
27	SP1	chr17:66507795-66509615	A549	lung:	n/a	chr17:66508451-66508462 chr17:66508531-66508552 chr17:66508811-66508825 chr17:66508817-66508826 chr17:66508816-66508825
28	CHD2	chr17:66508081-66509153	HepG2	liver:	n/a	n/a
29	POLR2A	chr17:66507750-66509241	GM18526	blood:	n/a	n/a
30	SIN3AK20	chr17:66509107-66509504	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr17:66507711-66509423	K562	blood:	n/a	n/a
32	RCOR1	chr17:66509094-66509153	K562	blood:	n/a	n/a
33	POLR2A	chr17:66507603-66509616	SK-N-SH	brain:	n/a	n/a
34	YY1	chr17:66507832-66509225	ECC-1	luminal epithelium:	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
35	MAX	chr17:66507414-66509653	MCF-7	breast:	n/a	chr17:66508092-66508101 chr17:66508090-66508105 chr17:66508092-66508107 chr17:66508094-66508104
36	POLR2A	chr17:66507790-66509689	Hela-S3	cervix:	n/a	n/a
37	MXI1	chr17:66506146-66510554	SK-N-SH	brain:	n/a	chr17:66508093-66508102 chr17:66508484-66508499 chr17:66508095-66508104
38	POLR2A	chr17:66507697-66509148	HEK293	kidney:	n/a	n/a
39	YY1	chr17:66507523-66509304	HepG2	liver:	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
40	POLR2A	chr17:66507794-66509488	K562	blood:	n/a	n/a
41	CHD1	chr17:66507161-66511463	IMR90	lung:	n/a	n/a
42	MXI1	chr17:66507307-66509876	GM12878	blood:	n/a	chr17:66508093-66508102 chr17:66508484-66508499 chr17:66508095-66508104
43	MAX	chr17:66507516-66509143	SK-N-SH	brain:	n/a	chr17:66508092-66508101 chr17:66508090-66508105 chr17:66508092-66508107 chr17:66508094-66508104
44	YY1	chr17:66508236-66509186	K562	blood:	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
45	UBTF	chr17:66507518-66509398	K562	blood:	n/a	n/a
46	MYC	chr17:66507716-66509541	K562	blood:	n/a	chr17:66508092-66508101 chr17:66508090-66508105 chr17:66508092-66508107 chr17:66508094-66508104
47	SIN3AK20	chr17:66507472-66509616	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr17:66507785-66509192	Raji	blood:	n/a	n/a
49	POLR2A	chr17:66508358-66509224	U87	brain:	n/a	n/a
50	SIN3A	chr17:66507714-66509579	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:66508673..66509254-chr6:35436145..35436972,2	Hela-S3	cervix:
2	chr15:81281716..81282444-chr17:66508534..66509364,2	Hela-S3	cervix:
3	chr17:65820674..65823268-chr17:66508486..66510670,2	MCF-7	breast:
4	chr1:155579581..155580433-chr17:66508628..66509408,2	Hela-S3	cervix:
5	chr17:66507304..66510193-chr5:1344921..1346652,2	MCF-7	breast:
6	chr17:66286763..66288590-chr17:66507383..66509365,2	MCF-7	breast:
7	chr17:66031856..66033575-chr17:66508155..66509939,2	MCF-7	breast:
8	chr17:66287636..66289963-chr17:66508320..66510109,2	K562	blood:
9	chr17:66507070..66510931-chr17:66511371..66513422,6	K562	blood:
10	chr17:66507858..66510140-chr17:66521050..66524441,3	K562	blood:
11	chr17:66451996..66456192-chr17:66506725..66511948,5	MCF-7	breast:
12	chr17:65988026..65990117-chr17:66506975..66509673,3	K562	blood:
13	chr17:66452513..66457853-chr17:66506674..66510981,7	MCF-7	breast:
14	chr17:66506755..66509358-chr17:66521590..66523476,3	K562	blood:

Variant related genes	Relation type
PRKAR1A	TF binding region
ENSG00000182481	Chromatin interaction
ENSG00000108932	Chromatin interaction
ENSG00000049656	Chromatin interaction
ENSG00000198755	Chromatin interaction
ENSG00000117899	Chromatin interaction
ENSG00000171634	Chromatin interaction
ENSG00000186665	Chromatin interaction
ENSG00000232519	Chromatin interaction
ENSG00000070540	Chromatin interaction
ENSG00000141337	Chromatin interaction
ENSG00000125459	Chromatin interaction
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10445232	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11651687	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11653616	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11657811	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12449539	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12453086	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302233	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3785906	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4281788	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58489712	0.96[ASN][1000 genomes]
rs7977	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9892782	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9913595	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9925	0.85[EUR][1000 genomes];0.95[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	chr17:66507400-66509200	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr17:66507400-66509800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:66507400-66509800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr17:66507400-66509800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr17:66507400-66510000	Active TSS	Brain Substantia Nigra	brain
10	chr17:66507400-66510200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr17:66507400-66510200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr17:66507400-66510200	Active TSS	Brain Cingulate Gyrus	brain
13	chr17:66507400-66510400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr17:66507400-66510400	Active TSS	Muscle Satellite Cultured Cells	--
15	chr17:66507400-66510600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:66507400-66510600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr17:66507400-66511000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr17:66507400-66511000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr17:66507400-66511000	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr17:66507400-66511400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr17:66507400-66513600	Active TSS	Right Ventricle	heart
22	chr17:66507600-66509400	Active TSS	Primary T cells from cord blood	blood
23	chr17:66507600-66509400	Active TSS	Fetal Brain Male	brain
24	chr17:66507600-66509600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:66507600-66509600	Active TSS	Gastric	stomach
26	chr17:66507600-66509600	Active TSS	Lung	lung
27	chr17:66507600-66509800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr17:66507600-66509800	Active TSS	Brain Angular Gyrus	brain
29	chr17:66507600-66509800	Active TSS	Brain Hippocampus Middle	brain
30	chr17:66507600-66510000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr17:66507600-66510000	Active TSS	Fetal Brain Female	brain
32	chr17:66507600-66510000	Bivalent/Poised TSS	HepG2	liver
33	chr17:66507600-66510200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr17:66507600-66510200	Active TSS	Fetal Kidney	kidney
35	chr17:66507600-66510400	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr17:66507600-66510400	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr17:66507600-66510400	Active TSS	Fetal Intestine Large	intestine
38	chr17:66507600-66510400	Active TSS	Hela-S3	cervix
39	chr17:66507600-66510600	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr17:66507600-66510800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr17:66507600-66510800	Active TSS	NHDF-Ad	bronchial
42	chr17:66507600-66511000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:66507600-66511200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr17:66507600-66511200	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr17:66507600-66511200	Active TSS	Left Ventricle	heart
46	chr17:66507600-66511400	Active TSS	Aorta	Aorta
47	chr17:66507600-66511600	Active TSS	Ovary	ovary
48	chr17:66507800-66509200	Active TSS	Primary B cells from peripheral blood	blood
49	chr17:66507800-66509200	Active TSS	Primary T cells fromperipheralblood	blood
50	chr17:66507800-66509200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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