Variant report

Variant	rs3746278
Chromosome Location	chr19:36233470-36233471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:117)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:117 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr19:36233196-36233568	GM12878	blood:	n/a	n/a
2	YY1	chr19:36233195-36233756	K562	blood:	n/a	n/a
3	YY1	chr19:36233102-36233815	GM12892	blood:	n/a	n/a
4	TBL1XR1	chr19:36233049-36233636	GM12878	blood:	n/a	n/a
5	MYC	chr19:36233217-36233574	NB4	blood:	n/a	n/a
6	CHD1	chr19:36233007-36233690	GM12878	blood:	n/a	n/a
7	RELA	chr19:36233138-36233633	GM10847	blood:	n/a	n/a
8	POLR2A	chr19:36233020-36234027	HL-60	blood:	n/a	n/a
9	NFIC	chr19:36232914-36233914	GM12878	blood:	n/a	n/a
10	TAF1	chr19:36233072-36233601	GM12878	blood:	n/a	n/a
11	PAX5	chr19:36232942-36233754	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:36233075-36233689	GM18951	blood:	n/a	n/a
13	SP1	chr19:36233120-36233594	GM12878	blood:	n/a	n/a
14	EP300	chr19:36233192-36233567	GM12878	blood:	n/a	n/a
15	TCF12	chr19:36233197-36233529	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:36233043-36233967	GM18505	blood:	n/a	n/a
17	POLR2A	chr19:36233003-36233874	GM19193	blood:	n/a	n/a
18	TAF1	chr19:36233165-36233562	GM12892	blood:	n/a	n/a
19	RELA	chr19:36233108-36233719	GM19099	blood:	n/a	n/a
20	EP300	chr19:36232988-36233915	GM12878	blood:	n/a	n/a
21	EBF1	chr19:36233027-36233801	GM12878	blood:	n/a	n/a
22	ELF1	chr19:36233055-36233910	GM12878	blood:	n/a	n/a
23	BCL11A	chr19:36233108-36233605	GM12878	blood:	n/a	n/a
24	TBP	chr19:36232986-36233657	GM12878	blood:	n/a	n/a
25	EGR1	chr19:36233222-36233536	GM12878	blood:	n/a	chr19:36233386-36233397 chr19:36233386-36233400
26	YY1	chr19:36233199-36233800	GM12878	blood:	n/a	n/a
27	RELA	chr19:36233013-36233678	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:36227197-36234067	GM12891	blood:	n/a	n/a
29	EGR1	chr19:36233230-36233528	GM12878	blood:	n/a	chr19:36233386-36233397 chr19:36233386-36233400
30	POU2F2	chr19:36233058-36233626	GM12878	blood:	n/a	n/a
31	TAF1	chr19:36233151-36233563	GM12891	blood:	n/a	n/a
32	SPI1	chr19:36233173-36233572	GM12891	blood:	n/a	n/a
33	POLR2A	chr19:36233054-36233919	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:36233004-36233989	GM12878	blood:	n/a	n/a
35	EBF1	chr19:36233044-36233594	GM12878	blood:	n/a	n/a
36	TCF3	chr19:36233101-36233567	GM12878	blood:	n/a	n/a
37	MEF2A	chr19:36233066-36233648	GM12878	blood:	n/a	n/a
38	BCLAF1	chr19:36233034-36233818	GM12878	blood:	n/a	n/a
39	POU2F2	chr19:36233016-36233759	GM12891	blood:	n/a	n/a
40	BHLHE40	chr19:36233165-36233574	GM12878	blood:	n/a	n/a
41	TCF3	chr19:36233240-36233484	GM12878	blood:	n/a	n/a
42	WRNIP1	chr19:36233063-36233816	GM12878	blood:	n/a	n/a
43	CEBPB	chr19:36233128-36233688	GM12878	blood:	n/a	n/a
44	RELA	chr19:36233115-36233725	GM18526	blood:	n/a	n/a
45	RUNX3	chr19:36232987-36233864	GM12878	blood:	n/a	n/a
46	TCF12	chr19:36233214-36233541	GM12878	blood:	n/a	n/a
47	RXRA	chr19:36233119-36233536	GM12878	blood:	n/a	chr19:36233160-36233180 chr19:36233164-36233177
48	ZEB1	chr19:36233187-36233515	GM12878	blood:	n/a	n/a
49	MAX	chr19:36233172-36233596	NB4	blood:	n/a	n/a
50	BCL3	chr19:36233146-36233534	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:36233447-36233497	HEK293	kidney:	embryo
2	chr19:36233447-36233497	SK-N-SH_RA	brain:	n/a
3	chr19:36233469-36233519	T-47D	breast:	n/a
4	chr19:36233469-36233519	ovcar-3	ovarian:	n/a
5	chr19:36233447-36233497	ProgFib	skin:	n/a
6	chr19:36233469-36233519	NHBE	bronchial:	n/a
7	chr19:36233469-36233519	NB4	blood:	n/a
8	chr19:36233447-36233497	SK-N-SH	brain:	n/a
9	chr19:36233447-36233497	NHBE	bronchial:	n/a
10	chr19:36233447-36233497	BE2_C	brain:	n/a
11	chr19:36233469-36233519	AG10803	skin:	n/a
12	chr19:36233447-36233497	GM19239	blood:	n/a
13	chr19:36233447-36233497	HEEpiC	esophagus:	n/a
14	chr19:36233447-36233497	RPTEC	kidney:	n/a
15	chr19:36233469-36233519	AG09309	skin:	n/a
16	chr19:36233469-36233519	HPAEpiC	pulmonary alveolar:	n/a
17	chr19:36233469-36233519	HNPCEpiC	eye:	n/a
18	chr19:36233447-36233497	HPAEpiC	pulmonary alveolar:	n/a
19	chr19:36233469-36233519	AoSMC	blood vessel:	n/a
20	chr19:36233469-36233519	Caco-2	colon:	n/a
21	chr19:36233447-36233497	HIPEpiC	eye:	n/a
22	chr19:36233469-36233519	IMR90	lung:	fetal
23	chr19:36233469-36233519	HCF	heart:	n/a
24	chr19:36233469-36233519	HepG2	liver:	n/a
25	chr19:36233469-36233519	SKMC	muscle:	n/a
26	chr19:36233447-36233497	MCF10A-Er-Src	breast:	n/a
27	chr19:36233447-36233497	HRCEpiC	kidney:	n/a
28	chr19:36233469-36233519	SK-N-MC	brain:	n/a
29	chr19:36233469-36233519	HCM	heart:	n/a
30	chr19:36233469-36233519	NH-A	brain:	n/a
31	chr19:36233469-36233519	HUVEC	blood vessel:	n/a
32	chr19:36233469-36233519	SK-N-SH_RA	brain:	n/a
33	chr19:36233447-36233497	NB4	blood:	n/a
34	chr19:36233447-36233497	HCPEpiC	choroid plexus:	n/a
35	chr19:36233469-36233519	NHDF-neo	bronchial:	n/a
36	chr19:36233469-36233519	SK-N-SH	brain:	n/a
37	chr19:36233447-36233497	HepG2	liver:	n/a
38	chr19:36233447-36233497	MCF-7	breast:	n/a
39	chr19:36233447-36233497	HCM	heart:	n/a
40	chr19:36233469-36233519	HIPEpiC	eye:	n/a
41	chr19:36233469-36233519	HMEC	breast:	n/a
42	chr19:36233469-36233519	H1-hESC	embryonic stem cell:	embryo
43	chr19:36233447-36233497	HRPEpiC	eye:	n/a
44	chr19:36233469-36233519	BJ	skin:	n/a
45	chr19:36233447-36233497	GM06990	blood:	n/a
46	chr19:36233447-36233497	HAEpiC	amniotic membrane:	n/a
47	chr19:36233447-36233497	NT2-D1	testis:	n/a
48	chr19:36233469-36233519	AG04450	lung:	fetal
49	chr19:36233447-36233497	HUVEC	blood vessel:	n/a
50	chr19:36233469-36233519	U87	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36205476..36213390-chr19:36226310..36233646,27	MCF-7	breast:
2	chr19:36231491..36233720-chr19:36248400..36250494,2	MCF-7	breast:

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-U2AF1L4-1	chr19:36233430-36234805	NONHSAT065899
2	lnc-U2AF1L4-1	chr19:36233433-36234106	NONHSAT065900
3	lnc-U2AF1L4-1	chr19:36233434-36234805	NONHSAT065902
4	lnc-U2AF1L4-1	chr19:36233428-36233704	NR_110173
5	lnc-U2AF1L4-1	chr19:36233428-36233704	NR_110171
6	lnc-U2AF1L4-1	chr19:36233428-36233704	NR_110172
7	lnc-U2AF1L4-1	chr19:36233433-36233704	NONHSAT065901

No data

Variant related genes	Relation type
IGFLR1	TF binding region
PSENEN	TF binding region
ENSG00000188223	TF binding region
ENSG00000188223	CpG island
PSENEN	CpG island
IGFLR1	CpG island
ENSG00000167595	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000004776	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs107878	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11084828	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11667696	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670414	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11671520	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11672164	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12151356	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12609803	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17776911	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293687	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787051	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3848663	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3885794	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3885795	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4806197	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4806198	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4806201	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4806202	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58561864	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66747537	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv515536	chr19:36219525-36240960	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36230800-36234000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr19:36230800-36234000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
3	chr19:36230800-36234000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr19:36230800-36234000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:36230800-36234000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:36230800-36234200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr19:36230800-36234400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr19:36231000-36234000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr19:36231200-36233800	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr19:36231400-36235200	Weak transcription	Fetal Heart	heart
11	chr19:36231800-36234000	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr19:36231800-36234000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:36231800-36234200	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr19:36232000-36234800	Weak transcription	Gastric	stomach
15	chr19:36232200-36233800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr19:36232200-36234000	Active TSS	Duodenum Mucosa	Duodenum
17	chr19:36232200-36234800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:36232200-36234800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:36232200-36234800	Weak transcription	Fetal Kidney	kidney
20	chr19:36232200-36234800	Weak transcription	Right Ventricle	heart
21	chr19:36232200-36234800	Weak transcription	Hela-S3	cervix
22	chr19:36232200-36235000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:36232200-36235000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:36232200-36235000	Weak transcription	Fetal Brain Male	brain
25	chr19:36232200-36235000	Weak transcription	Stomach Mucosa	stomach
26	chr19:36232200-36235000	Weak transcription	Osteobl	bone
27	chr19:36232200-36235200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:36232200-36235200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:36232200-36235200	Weak transcription	Aorta	Aorta
30	chr19:36232200-36235200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr19:36232200-36235200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr19:36232200-36235200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:36232200-36235200	Weak transcription	HMEC	breast
34	chr19:36232200-36235200	Weak transcription	HUVEC	blood vessel
35	chr19:36232200-36235200	Weak transcription	NH-A	brain
36	chr19:36232200-36235200	Weak transcription	NHDF-Ad	bronchial
37	chr19:36232400-36234000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr19:36232400-36234200	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr19:36232400-36234800	Weak transcription	Right Atrium	heart
40	chr19:36232400-36235000	Weak transcription	Fetal Brain Female	brain
41	chr19:36232400-36235200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr19:36232400-36235200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr19:36232400-36235200	Weak transcription	Small Intestine	intestine
44	chr19:36232400-36235400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:36232400-36235400	Weak transcription	Psoas Muscle	Psoas
46	chr19:36232600-36233800	Enhancers	K562	blood
47	chr19:36232600-36234000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:36232600-36234000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:36232600-36234000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr19:36232600-36234000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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