Variant report

Variant	rs66538320
Chromosome Location	chr3:156392135-156392136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:664)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:664 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr3:156391717-156392220	A549	lung:	n/a	n/a
2	ZNF384	chr3:156391727-156392588	K562	blood:	n/a	n/a
3	POLR2A	chr3:156391646-156392735	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr3:156391697-156392713	K562	blood:	n/a	n/a
5	POLR2A	chr3:156392044-156392561	SK-N-SH	brain:	n/a	n/a
6	ZMIZ1	chr3:156391645-156392679	K562	blood:	n/a	n/a
7	TBP	chr3:156391749-156392799	HepG2	liver:	n/a	n/a
8	SMARCC1	chr3:156391667-156393085	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:156391867-156392663	SK-N-SH	brain:	n/a	n/a
10	ESR1	chr3:156391829-156392290	ECC-1	luminal epithelium:	n/a	chr3:156392046-156392061
11	FOXA1	chr3:156391645-156392432	HepG2	liver:	n/a	chr3:156391973-156391985
12	YY1	chr3:156391670-156392600	ECC-1	luminal epithelium:	n/a	chr3:156391875-156391886 chr3:156392315-156392329 chr3:156392439-156392448
13	MAX	chr3:156391520-156392851	MCF-7	breast:	n/a	n/a
14	RCOR1	chr3:156391602-156392546	GM12878	blood:	n/a	n/a
15	TEAD4	chr3:156391707-156392530	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr3:156391469-156392784	MCF-7	breast:	n/a	n/a
17	POLR2A	chr3:156391948-156392572	A549	lung:	n/a	n/a
18	EP300	chr3:156391670-156392557	H1-hESC	embryonic stem cell:	n/a	n/a
19	FOXA1	chr3:156391678-156392230	HepG2	liver:	n/a	chr3:156391973-156391985
20	TAF1	chr3:156391932-156392768	K562	blood:	n/a	n/a
21	POLR2A	chr3:156391542-156392766	H1-neurons	neurons:	n/a	n/a
22	IRF3	chr3:156391751-156392159	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:156391392-156394830	MCF10A-Er-Src	breast:	n/a	n/a
24	ATF1	chr3:156391740-156392525	K562	blood:	n/a	n/a
25	POLR2A	chr3:156391750-156392837	Gliobla	brain:	n/a	n/a
26	MXI1	chr3:156391527-156396530	IMR90	lung:	n/a	n/a
27	RAD21	chr3:156391634-156392399	HepG2	liver:	n/a	chr3:156392246-156392256
28	POLR2A	chr3:156391586-156392716	H1-neurons	neurons:	n/a	n/a
29	CUX1	chr3:156391773-156392212	K562	blood:	n/a	n/a
30	EP300	chr3:156391632-156392443	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:156391803-156392681	NB4	blood:	n/a	n/a
32	CTCF	chr3:156391594-156393671	GM12878	blood:	n/a	chr3:156393431-156393449 chr3:156393432-156393448 chr3:156392243-156392256
33	SP1	chr3:156391619-156392643	A549	lung:	n/a	chr3:156392324-156392336 chr3:156392249-156392259 chr3:156392248-156392260 chr3:156392169-156392179 chr3:156392169-156392179 chr3:156392250-156392259 chr3:156392295-156392305 chr3:156392248-156392260
34	CTCF	chr3:156391661-156392697	IMR90	lung:	n/a	chr3:156392243-156392256
35	RELA	chr3:156391567-156392600	GM18505	blood:	n/a	n/a
36	NR3C1	chr3:156391804-156392232	A549	lung:	n/a	n/a
37	TCF12	chr3:156391600-156392208	H1-hESC	embryonic stem cell:	n/a	n/a
38	RAD21	chr3:156391256-156394283	SK-N-SH	brain:	n/a	chr3:156392246-156392256 chr3:156393667-156393674
39	BCL11A	chr3:156391698-156392202	GM12878	blood:	n/a	chr3:156391838-156391851
40	SIN3A	chr3:156391673-156393956	H1-hESC	embryonic stem cell:	n/a	chr3:156393307-156393318 chr3:156393409-156393418
41	PML	chr3:156391671-156392740	MCF-7	breast:	n/a	n/a
42	CTCF	chr3:156391539-156392326	A549	lung:	n/a	chr3:156392243-156392256
43	CTCF	chr3:156391761-156392263	Medullo	brain:	n/a	chr3:156392243-156392256
44	POLR2A	chr3:156391729-156392974	A549	lung:	n/a	n/a
45	YY1	chr3:156391592-156392572	GM12878	blood:	n/a	chr3:156391875-156391886 chr3:156392315-156392329 chr3:156392439-156392448
46	POLR2A	chr3:156391886-156392683	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr3:156391537-156394159	HL-60	blood:	n/a	n/a
48	TAF1	chr3:156391788-156392607	H1-hESC	embryonic stem cell:	n/a	n/a
49	YY1	chr3:156392030-156392545	HCT-116	colon:	n/a	chr3:156392315-156392329 chr3:156392439-156392448
50	RCOR1	chr3:156391586-156392741	HepG2	liver:	n/a	n/a

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:85741939..85742635-chr3:156391987..156392721,2	Hela-S3	cervix:
2	chr3:156390449..156395705-chr3:156876136..156879645,10	MCF-7	breast:
3	chr3:156391507..156394071-chr3:156396999..156400389,4	MCF-7	breast:
4	chr3:156391970..156394815-chr3:156799472..156801135,3	MCF-7	breast:
5	chr3:156391993..156392722-chr3:156534538..156535088,2	MCF-7	breast:
6	chr3:156270771..156274735-chr3:156390391..156394038,18	K562	blood:
7	chr3:156390967..156393612-chr3:156877452..156879722,5	K562	blood:
8	chr3:156391796..156394617-chr3:156542307..156544876,4	K562	blood:
9	chr3:156268357..156274553-chr3:156389283..156394606,15	MCF-7	breast:
10	chr3:156391432..156392673-chr3:156799216..156800183,12	MCF-7	breast:
11	chr3:156391537..156393857-chr3:156543728..156545632,2	K562	blood:
12	chr3:156389452..156396391-chr3:156801976..156809206,19	MCF-7	breast:
13	chr2:136287860..136288544-chr3:156391990..156392562,2	Hela-S3	cervix:
14	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
15	chr3:156391529..156394159-chr3:156805680..156808214,2	K562	blood:
16	chr3:156391768..156393756-chr3:156838455..156841015,3	K562	blood:
17	chr12:92538568..92539165-chr3:156391568..156392141,2	Hela-S3	cervix:
18	chr3:156272378..156273447-chr3:156391539..156392497,3	NB4	blood:
19	chr17:79669724..79670450-chr3:156392050..156392769,2	Hela-S3	cervix:
20	chr3:156392071..156392661-chr3:160282867..160283573,2	NB4	blood:
21	chr3:156392014..156393878-chr3:156839101..156841015,2	K562	blood:
22	chr3:156391446..156393768-chr3:156890974..156892598,2	MCF-7	breast:
23	chr3:156391356..156392486-chr3:156799238..156800133,4	K562	blood:
24	chr3:156269857..156276442-chr3:156389324..156394083,11	MCF-7	breast:
25	chr20:44044560..44045442-chr3:156392012..156392666,2	Hela-S3	cervix:
26	chr3:156391251..156395598-chr3:156875832..156879722,8	K562	blood:
27	chr3:156272675..156273484-chr3:156391601..156392336,4	MCF-7	breast:
28	chr3:156391825..156392818-chr4:140005100..140005618,2	Hela-S3	cervix:
29	chr3:156391202..156392503-chr3:156799357..156800312,5	MCF-7	breast:
30	chr3:156391482..156392232-chr7:10979248..10979918,2	HCT-116	colon:
31	chr3:156260735..156275674-chr3:156389736..156397850,44	K562	blood:
32	chr3:156389670..156395497-chr3:156530360..156537244,22	MCF-7	breast:
33	chr3:156390293..156396385-chr3:156542364..156548172,18	MCF-7	breast:
34	chr3:156390535..156395368-chr3:156542467..156546251,7	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-2	chr3:156391996-156392167	ENSG00000243926.1
2	lnc-SSR3-2	chr3:156391996-156393668	NONHSAT092857
3	lnc-SSR3-2	chr3:156390960-156393502	NONHSAT092861

No data

Variant related genes	Relation type
TIPARP-AS1	TF binding region
TIPARP	TF binding region
ENSG00000121988	Chromatin interaction
ENSG00000262049	Chromatin interaction
ENSG00000186432	Chromatin interaction
ENSG00000230457	Chromatin interaction
ENSG00000133639	Chromatin interaction
ENSG00000243629	Chromatin interaction
ENSG00000262660	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000189043	Chromatin interaction
ENSG00000183048	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000241135	Chromatin interaction
ENSG00000222675	Chromatin interaction
ENSG00000240875	Chromatin interaction
ENSG00000114850	Chromatin interaction
ENSG00000109381	Chromatin interaction
ENSG00000223653	Chromatin interaction
ENSG00000241544	Chromatin interaction
ENSG00000262814	Chromatin interaction
ENSG00000124155	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10428096	0.84[AFR][1000 genomes]
rs10454220	0.82[AFR][1000 genomes]
rs13061457	0.83[ASN][1000 genomes]
rs1469536	0.81[ASN][1000 genomes]
rs34277251	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3851992	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[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	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs66538320	TIPARP-AS1	cis	Thyroid	GTEx
rs66538320	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156391000-156393000	Active TSS	Fetal Brain Male	brain
2	chr3:156391200-156392200	Flanking Active TSS	Dnd41	blood
3	chr3:156391200-156394000	Active TSS	Fetal Kidney	kidney
4	chr3:156391400-156392400	Active TSS	Brain Germinal Matrix	brain
5	chr3:156391400-156393400	Active TSS	Fetal Brain Female	brain
6	chr3:156391400-156393600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:156391400-156393600	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr3:156391400-156393800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:156391400-156393800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:156391400-156393800	Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr3:156391400-156393800	Active TSS	Brain Anterior Caudate	brain
12	chr3:156391400-156393800	Active TSS	Brain Hippocampus Middle	brain
13	chr3:156391400-156393800	Active TSS	Stomach Smooth Muscle	stomach
14	chr3:156391400-156394000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:156391400-156394000	Active TSS	Adipose Nuclei	Adipose
16	chr3:156391400-156394200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr3:156391400-156394200	Active TSS	Osteobl	bone
18	chr3:156391400-156394600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr3:156391400-156395000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr3:156391400-156395000	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:156391400-156395200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:156391400-156395200	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr3:156391400-156395200	Active TSS	Psoas Muscle	Psoas
24	chr3:156391600-156392200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:156391600-156392200	Flanking Active TSS	Fetal Thymus	thymus
26	chr3:156391600-156392200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr3:156391600-156392400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:156391600-156392600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:156391600-156393400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:156391600-156393600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:156391600-156393800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr3:156391600-156393800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:156391600-156393800	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr3:156391600-156393800	Active TSS	Fetal Intestine Large	intestine
35	chr3:156391600-156393800	Active TSS	Gastric	stomach
36	chr3:156391600-156393800	Active TSS	Pancreas	Pancrea
37	chr3:156391600-156393800	Active TSS	Thymus	Thymus
38	chr3:156391600-156394000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:156391600-156394000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr3:156391600-156394000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:156391600-156394000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:156391600-156394000	Active TSS	Brain Substantia Nigra	brain
43	chr3:156391600-156394000	Active TSS	Colon Smooth Muscle	Colon
44	chr3:156391600-156394000	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr3:156391600-156394000	Active TSS	Small Intestine	intestine
46	chr3:156391600-156394000	Active TSS	Spleen	Spleen
47	chr3:156391600-156394200	Active TSS	H1 Cell Line	embryonic stem cell
48	chr3:156391600-156394200	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr3:156391600-156394200	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr3:156391600-156394200	Active TSS	Colonic Mucosa	Colon

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