Variant report

Variant	rs13072132
Chromosome Location	chr3:47866161-47866162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:155)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:155 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr3:47866119-47866957	HepG2	liver:	n/a	n/a
2	RUNX3	chr3:47866075-47866911	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:47866136-47866812	IMR90	lung:	n/a	n/a
4	POLR2A	chr3:47866152-47866909	HEK293	kidney:	n/a	n/a
5	POLR2A	chr3:47866158-47867154	MCF-7	breast:	n/a	n/a
6	BCL3	chr3:47865979-47866428	A549	lung:	n/a	n/a
7	MAX	chr3:47866135-47866816	MCF-7	breast:	n/a	n/a
8	POLR2A	chr3:47865908-47867654	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr3:47866079-47867046	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:47866145-47866948	HCT-116	colon:	n/a	n/a
11	POLR2A	chr3:47866159-47866888	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:47866135-47866781	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr3:47862121-47869038	K562	blood:	n/a	n/a
14	GTF2F1	chr3:47866137-47866613	Hela-S3	cervix:	n/a	n/a
15	BCLAF1	chr3:47866103-47866834	K562	blood:	n/a	chr3:47866820-47866833
16	BHLHE40	chr3:47866023-47866638	HepG2	liver:	n/a	chr3:47866150-47866159 chr3:47866151-47866160 chr3:47866145-47866166 chr3:47866151-47866160 chr3:47866149-47866162
17	POLR2A	chr3:47866152-47866944	Hela-S3	cervix:	n/a	n/a
18	KAP1	chr3:47866029-47866828	HEK293	kidney:	n/a	n/a
19	HEY1	chr3:47866136-47866804	HepG2	liver:	n/a	chr3:47866496-47866511
20	MYC	chr3:47866151-47866800	A549	lung:	n/a	n/a
21	CTCF	chr3:47866160-47866310	HFF-Myc	foreskin:	n/a	n/a
22	POLR2A	chr3:47866111-47866828	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr3:47866119-47866779	HCT-116	colon:	n/a	n/a
24	POLR2A	chr3:47866142-47867179	K562	blood:	n/a	n/a
25	YY1	chr3:47865988-47867352	H1-hESC	embryonic stem cell:	n/a	chr3:47867244-47867253 chr3:47867333-47867344 chr3:47867333-47867342 chr3:47866749-47866758
26	PML	chr3:47865956-47867203	GM12878	blood:	n/a	n/a
27	TBP	chr3:47866149-47866647	Hela-S3	cervix:	n/a	n/a
28	MAX	chr3:47866108-47867166	ECC-1	luminal epithelium:	n/a	chr3:47866825-47866835
29	NFIC	chr3:47865868-47866772	ECC-1	luminal epithelium:	n/a	n/a
30	KAP1	chr3:47866113-47866637	U2OS	brain:	n/a	n/a
31	POLR2A	chr3:47866078-47866786	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr3:47866058-47867283	GM12892	blood:	n/a	n/a
33	POLR2A	chr3:47866159-47866725	HepG2	liver:	n/a	n/a
34	BHLHE40	chr3:47866074-47866643	GM12878	blood:	n/a	chr3:47866150-47866159 chr3:47866151-47866160 chr3:47866145-47866166 chr3:47866151-47866160 chr3:47866149-47866162
35	STAT1	chr3:47866128-47866727	GM12878	blood:	n/a	n/a
36	CREB1	chr3:47866156-47866835	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr3:47865979-47866959	U87	brain:	n/a	n/a
38	MAX	chr3:47865948-47867131	HepG2	liver:	n/a	chr3:47866825-47866835
39	CTCF	chr3:47866157-47866981	H1-hESC	embryonic stem cell:	n/a	n/a
40	HCFC1	chr3:47866126-47867617	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr3:47866034-47867192	GM12892	blood:	n/a	n/a
42	POLR2A	chr3:47866051-47866820	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr3:47866047-47867226	H1-hESC	embryonic stem cell:	n/a	n/a
44	RELA	chr3:47866139-47866802	GM15510	blood:	n/a	n/a
45	MAX	chr3:47866117-47866724	SK-N-SH	brain:	n/a	n/a
46	FOXM1	chr3:47866097-47867023	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:47866145-47866805	SK-N-SH	brain:	n/a	n/a
48	CHD2	chr3:47866156-47866710	K562	blood:	n/a	n/a
49	STAT5A	chr3:47866014-47866815	GM12878	blood:	n/a	n/a
50	POLR2A	chr3:47865946-47867385	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:47866155-47866205	ECC-1	luminal epithelium:	n/a
2	chr3:47866155-47866205	HRCEpiC	kidney:	n/a
3	chr3:47866155-47866205	U87	brain:	n/a
4	chr3:47866155-47866205	AG10803	skin:	n/a
5	chr3:47866155-47866205	NB4	blood:	n/a
6	chr3:47866155-47866205	HepG2	liver:	n/a
7	chr3:47866155-47866205	GM12892	blood:	n/a
8	chr3:47866155-47866205	PrEC	prostate:	n/a
9	chr3:47866155-47866205	AG04449	skin:	fetal
10	chr3:47866155-47866205	Jurkat	blood:	n/a
11	chr3:47866155-47866205	MCF10A-Er-Src	breast:	n/a
12	chr3:47866155-47866205	MCF-7	breast:	n/a
13	chr3:47866155-47866205	BJ	skin:	n/a
14	chr3:47866155-47866205	T-47D	breast:	n/a
15	chr3:47866155-47866205	SK-N-SH_RA	brain:	n/a
16	chr3:47866155-47866205	NH-A	brain:	n/a
17	chr3:47866155-47866205	SKMC	muscle:	n/a
18	chr3:47866155-47866205	K562	blood:	n/a
19	chr3:47866155-47866205	Caco-2	colon:	n/a
20	chr3:47866155-47866205	AoSMC	blood vessel:	n/a
21	chr3:47866155-47866205	HEK293	kidney:	embryo
22	chr3:47866155-47866205	NT2-D1	testis:	n/a
23	chr3:47866155-47866205	AG04450	lung:	fetal
24	chr3:47866155-47866205	GM12878	blood:	n/a
25	chr3:47866155-47866205	RPTEC	kidney:	n/a
26	chr3:47866155-47866205	HAEpiC	amniotic membrane:	n/a
27	chr3:47866155-47866205	SAEC	small airway:	n/a
28	chr3:47866155-47866205	AG09319	gingival:	n/a
29	chr3:47866155-47866205	HMEC	breast:	n/a
30	chr3:47866155-47866205	PANC-1	pancreas:	n/a
31	chr3:47866155-47866205	HL-60	blood:	n/a
32	chr3:47866155-47866205	HRE	kidney:	n/a
33	chr3:47866155-47866205	HNPCEpiC	eye:	n/a
34	chr3:47866155-47866205	HCF	heart:	n/a
35	chr3:47866155-47866205	HCM	heart:	n/a
36	chr3:47866155-47866205	HUVEC	blood vessel:	n/a
37	chr3:47866155-47866205	CMK	blood:	n/a
38	chr3:47866155-47866205	SK-N-MC	brain:	n/a
39	chr3:47866155-47866205	NHDF-neo	bronchial:	n/a
40	chr3:47866155-47866205	HEEpiC	esophagus:	n/a
41	chr3:47866155-47866205	BE2_C	brain:	n/a
42	chr3:47866155-47866205	A549	lung:	n/a
43	chr3:47866155-47866205	LNCaP	prostate:	n/a
44	chr3:47866155-47866205	SK-N-SH	brain:	n/a
45	chr3:47866155-47866205	Hepatocyte	liver:	n/a
46	chr3:47866155-47866205	GM12891	blood:	n/a
47	chr3:47866155-47866205	HPAEpiC	pulmonary alveolar:	n/a
48	chr3:47866155-47866205	PFSK-1	brain:	n/a
49	chr3:47866155-47866205	Hela-S3	cervix:	n/a
50	chr3:47866155-47866205	HRPEpiC	eye:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47864865..47866925-chr3:48129196..48131775,2	MCF-7	breast:
2	chr3:47864742..47870552-chr3:47891000..47894370,6	K562	blood:
3	chr3:47841394..47846517-chr3:47861978..47869167,10	MCF-7	breast:
4	chr3:47421585..47423707-chr3:47865885..47867908,2	K562	blood:
5	chr3:47865438..47868063-chr3:47949472..47951050,2	K562	blood:
6	chr3:47844102..47845469-chr3:47866160..47867156,4	K562	blood:
7	chr3:47842553..47846144-chr3:47865369..47869227,6	MCF-7	breast:
8	chr3:47821721..47824833-chr3:47865723..47867890,4	K562	blood:
9	chr3:47421478..47423085-chr3:47865885..47868776,2	K562	blood:
10	chr3:47843809..47846911-chr3:47863750..47868075,7	K562	blood:
11	chr3:47843874..47846988-chr3:47863750..47867904,4	K562	blood:

No data

Variant related genes	Relation type
DHX30	TF binding region
DHX30	CpG island
ENSG00000076201	Chromatin interaction
ENSG00000173473	Chromatin interaction
ENSG00000260236	Chromatin interaction
ENSG00000047849	Chromatin interaction
ENSG00000221585	Chromatin interaction
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1060407	0.81[CEU][hapmap]
rs11707679	0.81[CEU][hapmap]
rs11709289	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17785248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs319682	0.81[CEU][hapmap]
rs319696	0.81[CEU][hapmap]
rs34448818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34507589	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35012836	0.82[AMR][1000 genomes]
rs4858871	0.81[CEU][hapmap]
rs5016900	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62260764	0.81[EUR][1000 genomes]
rs6763824	0.92[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap]
rs7430913	0.86[CEU][hapmap]
rs777015	0.81[CEU][hapmap]
rs796566	0.84[CEU][hapmap]
rs810334	0.81[CEU][hapmap]

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	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs13072132	ZNF589	cis	Esophagus Muscularis	GTEx
rs13072132	CDC25A	cis	cerebellum	SCAN
rs13072132	NME6	cis	Esophagus Muscularis	GTEx
rs13072132	MRPS18AP1	cis	Artery Tibial	GTEx
rs13072132	MRPS18AP1	cis	Thyroid	GTEx
rs13072132	ZNF589	cis	cerebellum	SCAN
rs13072132	ZNF589	cis	Artery Tibial	GTEx
rs13072132	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs13072132	MRPS18AP1	cis	Nerve Tibial	GTEx
rs13072132	CDC25A	cis	Muscle Skeletal	GTEx
rs13072132	SMARCC1	cis	cerebellum	SCAN
rs13072132	ZNF589	cis	Nerve Tibial	GTEx
rs13072132	ZNF589	cis	parietal	SCAN
rs13072132	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs13072132	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs13072132	MAP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47845600-47866200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:47845600-47866600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:47852600-47866200	Weak transcription	Psoas Muscle	Psoas
4	chr3:47860800-47866200	Weak transcription	Primary B cells from cord blood	blood
5	chr3:47861400-47866200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:47861400-47866200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:47861400-47866400	Weak transcription	Aorta	Aorta
8	chr3:47861600-47866200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:47863800-47866200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:47864400-47866200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:47865200-47866200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:47865200-47866200	Enhancers	Liver	Liver
13	chr3:47865800-47866200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:47865800-47866200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr3:47865800-47866200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:47865800-47866200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr3:47865800-47866200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:47865800-47866200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr3:47865800-47866200	Enhancers	Brain Angular Gyrus	brain
20	chr3:47865800-47866200	Enhancers	Brain Substantia Nigra	brain
21	chr3:47865800-47866200	Enhancers	Duodenum Mucosa	Duodenum
22	chr3:47865800-47866200	Enhancers	Left Ventricle	heart
23	chr3:47865800-47866200	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr3:47865800-47866200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:47865800-47866400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:47865800-47866400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:47865800-47866400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:47865800-47866400	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr3:47865800-47866400	Flanking Active TSS	Dnd41	blood
30	chr3:47865800-47866400	Flanking Active TSS	Hela-S3	cervix
31	chr3:47865800-47866600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr3:47865800-47866800	Enhancers	Stomach Mucosa	stomach
33	chr3:47865800-47867400	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr3:47865800-47867400	Enhancers	Fetal Heart	heart
35	chr3:47866000-47866200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:47866000-47866200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:47866000-47866200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr3:47866000-47866200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:47866000-47866200	Enhancers	Primary B cells from peripheral blood	blood
40	chr3:47866000-47866200	Enhancers	Primary T cells from cord blood	blood
41	chr3:47866000-47866200	Enhancers	Primary hematopoietic stem cells	blood
42	chr3:47866000-47866200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:47866000-47866200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:47866000-47866200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:47866000-47866200	Enhancers	Colonic Mucosa	Colon
46	chr3:47866000-47866200	Enhancers	Esophagus	oesophagus
47	chr3:47866000-47866200	Flanking Active TSS	Fetal Brain Female	brain
48	chr3:47866000-47866200	Enhancers	Fetal Intestine Large	intestine
49	chr3:47866000-47866200	Enhancers	Gastric	stomach
50	chr3:47866000-47866200	Enhancers	Lung	lung

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