Variant report

Variant	rs4887092
Chromosome Location	chr15:79043675-79043676
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	CTCF	chr15:79043394-79043777	H1-hESC	embryonic stem cell:	n/a	chr15:79043461-79043474
2	SMC3	chr15:79043388-79043760	K562	blood:	n/a	n/a
3	CTCF	chr15:79043444-79043727	Kidney_OC	kidney:	n/a	chr15:79043461-79043474
4	CTCF	chr15:79043434-79043715	LNCaP	prostate:	n/a	chr15:79043461-79043474
5	RAD21	chr15:79043354-79043732	SK-N-SH_RA	brain:	n/a	n/a
6	CTCF	chr15:79043290-79043827	MCF-7	breast:	n/a	chr15:79043461-79043474
7	RAD21	chr15:79043392-79043754	A549	lung:	n/a	n/a
8	HCFC1	chr15:79043059-79043907	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr15:79043540-79043690	GM12872	blood:	n/a	n/a
10	MAZ	chr15:79043403-79043722	GM12878	blood:	n/a	chr15:79043538-79043548
11	CTCF	chr15:79043424-79043715	A549	lung:	n/a	chr15:79043461-79043474
12	EP300	chr15:79043557-79043707	K562	blood:	n/a	n/a
13	CTCF	chr15:79043560-79043710	HCM	heart:	n/a	n/a
14	CREB1	chr15:79043426-79043691	A549	lung:	n/a	n/a
15	CTCF	chr15:79043451-79043689	HepG2	liver:	n/a	chr15:79043461-79043474
16	POU2F2	chr15:79043410-79043683	GM12878	blood:	n/a	n/a
17	SMC3	chr15:79043410-79043760	GM12878	blood:	n/a	n/a
18	YY1	chr15:79043411-79043720	GM12878	blood:	n/a	n/a
19	CTCF	chr15:79043420-79043750	Lung_OC	lung:	n/a	chr15:79043461-79043474
20	CTCF	chr15:79043540-79043690	NHDF-neo	bronchial:	n/a	n/a
21	CTCF	chr15:79043441-79043769	HepG2	liver:	n/a	chr15:79043461-79043474
22	CTCF	chr15:79043394-79043745	GM19239	blood:	n/a	chr15:79043461-79043474
23	CTCF	chr15:79043459-79043709	GM10248	blood:	n/a	chr15:79043461-79043474
24	TEAD4	chr15:79043349-79043774	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr15:79043402-79043894	GM19238	blood:	n/a	chr15:79043461-79043474
26	CTCF	chr15:79043392-79043727	NHEK	skin:	n/a	chr15:79043461-79043474
27	CTCF	chr15:79043441-79043724	GM10266	blood:	n/a	chr15:79043461-79043474
28	CTCF	chr15:79043395-79043779	K562	blood:	n/a	chr15:79043461-79043474
29	CTCF	chr15:79043296-79043757	MCF-7	breast:	n/a	chr15:79043461-79043474
30	CTCF	chr15:79043540-79043690	HVMF	connective:	n/a	n/a
31	EP300	chr15:79043425-79043719	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr15:79043292-79043711	Hela-S3	cervix:	n/a	chr15:79043538-79043548
33	SP1	chr15:79043286-79043784	GM12878	blood:	n/a	chr15:79043538-79043548 chr15:79043483-79043493 chr15:79043537-79043549 chr15:79043502-79043513 chr15:79043483-79043493 chr15:79043537-79043548 chr15:79043537-79043549
34	RCOR1	chr15:79043436-79043688	K562	blood:	n/a	n/a
35	CHD2	chr15:79043394-79043720	Hela-S3	cervix:	n/a	n/a
36	SP1	chr15:79043199-79043798	A549	lung:	n/a	chr15:79043538-79043548 chr15:79043483-79043493 chr15:79043537-79043549 chr15:79043502-79043513 chr15:79043483-79043493 chr15:79043537-79043548 chr15:79043537-79043549
37	CTCF	chr15:79043423-79043715	MCF-7	breast:	n/a	chr15:79043461-79043474
38	ZBTB7A	chr15:79043486-79043678	K562	blood:	n/a	chr15:79043507-79043514
39	CTCF	chr15:79043580-79043730	BE2_C	brain:	n/a	n/a
40	CTCF	chr15:79043415-79043713	MCF-7	breast:	n/a	chr15:79043461-79043474
41	CTCF	chr15:79043560-79043710	GM12867	blood:	n/a	n/a
42	POU2F2	chr15:79043333-79043751	GM12878	blood:	n/a	n/a
43	CTCF	chr15:79043420-79043710	Hela-S3	cervix:	n/a	chr15:79043461-79043474
44	CTCF	chr15:79043445-79043751	SK-N-SH_RA	brain:	n/a	chr15:79043461-79043474
45	BHLHE40	chr15:79043479-79043679	GM12878	blood:	n/a	n/a
46	MAZ	chr15:79043243-79043804	IMR90	lung:	n/a	chr15:79043538-79043548
47	RAD21	chr15:79043285-79043800	A549	lung:	n/a	n/a
48	EGR1	chr15:79043375-79043700	H1-hESC	embryonic stem cell:	n/a	chr15:79043478-79043492 chr15:79043479-79043493 chr15:79043480-79043490 chr15:79043477-79043492 chr15:79043537-79043551 chr15:79043502-79043516
49	CTCF	chr15:79043409-79043722	GM12878	blood:	n/a	chr15:79043461-79043474
50	RAD21	chr15:79043319-79043798	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:79043637-79043687	PANC-1	pancreas:	n/a
2	chr15:79043637-79043687	ProgFib	skin:	n/a
3	chr15:79043637-79043687	Caco-2	colon:	n/a
4	chr15:79043637-79043687	CMK	blood:	n/a
5	chr15:79043637-79043687	PrEC	prostate:	n/a
6	chr15:79043637-79043687	HAEpiC	amniotic membrane:	n/a
7	chr15:79043637-79043687	HCPEpiC	choroid plexus:	n/a
8	chr15:79043637-79043687	ECC-1	luminal epithelium:	n/a
9	chr15:79043637-79043687	PFSK-1	brain:	n/a
10	chr15:79043637-79043687	IMR90	lung:	fetal
11	chr15:79043637-79043687	GM12891	blood:	n/a
12	chr15:79043637-79043687	AoSMC	blood vessel:	n/a
13	chr15:79043637-79043687	HPAEpiC	pulmonary alveolar:	n/a
14	chr15:79043637-79043687	GM12878	blood:	n/a
15	chr15:79043637-79043687	Jurkat	blood:	n/a
16	chr15:79043637-79043687	HCM	heart:	n/a
17	chr15:79043637-79043687	AG09309	skin:	n/a
18	chr15:79043637-79043687	Hela-S3	cervix:	n/a
19	chr15:79043637-79043687	SK-N-SH_RA	brain:	n/a
20	chr15:79043637-79043687	HRPEpiC	eye:	n/a
21	chr15:79043637-79043687	U87	brain:	n/a
22	chr15:79043637-79043687	A549	lung:	n/a
23	chr15:79043637-79043687	HIPEpiC	eye:	n/a
24	chr15:79043637-79043687	RPTEC	kidney:	n/a
25	chr15:79043637-79043687	HMEC	breast:	n/a
26	chr15:79043637-79043687	AG10803	skin:	n/a
27	chr15:79043637-79043687	HEK293	kidney:	embryo
28	chr15:79043637-79043687	HNPCEpiC	eye:	n/a
29	chr15:79043637-79043687	HepG2	liver:	n/a
30	chr15:79043637-79043687	K562	blood:	n/a
31	chr15:79043637-79043687	T-47D	breast:	n/a
32	chr15:79043637-79043687	NB4	blood:	n/a
33	chr15:79043637-79043687	HEEpiC	esophagus:	n/a
34	chr15:79043637-79043687	H1-hESC	embryonic stem cell:	embryo
35	chr15:79043637-79043687	NHDF-neo	bronchial:	n/a
36	chr15:79043637-79043687	AG04449	skin:	fetal
37	chr15:79043637-79043687	ovcar-3	ovarian:	n/a
38	chr15:79043637-79043687	NT2-D1	testis:	n/a
39	chr15:79043637-79043687	MCF-7	breast:	n/a
40	chr15:79043637-79043687	HUVEC	blood vessel:	n/a
41	chr15:79043637-79043687	GM12892	blood:	n/a
42	chr15:79043637-79043687	GM19239	blood:	n/a
43	chr15:79043637-79043687	AG04450	lung:	fetal
44	chr15:79043637-79043687	NH-A	brain:	n/a
45	chr15:79043637-79043687	SAEC	small airway:	n/a
46	chr15:79043637-79043687	SK-N-MC	brain:	n/a
47	chr15:79043637-79043687	NHBE	bronchial:	n/a
48	chr15:79043637-79043687	SKMC	muscle:	n/a
49	chr15:79043637-79043687	HCT-116	colon:	n/a
50	chr15:79043637-79043687	Hepatocyte	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78774775..78775285-chr15:79043113..79043866,2	MCF-7	breast:
2	chr15:78591118..78593802-chr15:79042531..79044066,2	K562	blood:
3	chr15:78292186..78292985-chr15:79043320..79043997,6	MCF-7	breast:
4	chr15:78292246..78292984-chr15:79043169..79044003,5	MCF-7	breast:
5	chr15:78292248..78292748-chr15:79043024..79043675,2	Hela-S3	cervix:
6	chr15:78291849..78292957-chr15:79043056..79044329,6	K562	blood:
7	chr15:78910576..78911172-chr15:79043464..79043998,2	MCF-7	breast:
8	chr15:79006871..79007822-chr15:79043105..79043707,3	K562	blood:
9	chr15:78290955..78292806-chr15:79043518..79045037,2	MCF-7	breast:
10	chr15:78405703..78406239-chr15:79043526..79044041,2	K562	blood:
11	chr15:79006813..79007487-chr15:79043128..79043964,2	MCF-7	breast:
12	chr15:78292459..78292975-chr15:79043082..79043688,2	HCT-116	colon:
13	chr15:78910853..78911424-chr15:79043087..79043970,4	K562	blood:

Variant related genes	Relation type
ENSG00000238166	TF binding region
ENSG00000238166	CpG island
ENSG00000140395	Chromatin interaction
ENSG00000167202	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11072800	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632672	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633152	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11852909	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12148817	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899201	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12901228	0.81[ASN][1000 genomes]
rs12904489	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12906022	0.80[ASN][1000 genomes]
rs12906165	0.80[ASN][1000 genomes]
rs12906835	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906847	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12906977	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907207	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907432	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907536	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12910831	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12912245	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12913779	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12917502	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1383634	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1383635	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1825086	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1904920	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1964562	0.81[ASN][1000 genomes]
rs2017091	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2017297	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2046143	0.81[ASN][1000 genomes]
rs2219939	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2622821	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34019568	0.81[ASN][1000 genomes]
rs4887091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59414039	0.81[ASN][1000 genomes]
rs71402966	0.80[AMR][1000 genomes]
rs7176070	0.86[EUR][1000 genomes]
rs7177143	0.85[ASN][1000 genomes]
rs7182567	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182694	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182993	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755998	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8024939	0.85[ASN][1000 genomes]
rs8030090	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8030335	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79033000-79045000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:79040600-79060000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:79042800-79043800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:79042800-79043800	Enhancers	Liver	Liver
5	chr15:79042800-79044000	Enhancers	Brain Cingulate Gyrus	brain
6	chr15:79042800-79044000	Bivalent Enhancer	Fetal Stomach	stomach
7	chr15:79042800-79044000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr15:79042800-79045000	Enhancers	Fetal Heart	heart
9	chr15:79042800-79055400	Enhancers	Right Ventricle	heart
10	chr15:79043000-79043800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr15:79043000-79043800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:79043000-79043800	Active TSS	Colon Smooth Muscle	Colon
13	chr15:79043000-79043800	Enhancers	Duodenum Mucosa	Duodenum
14	chr15:79043000-79043800	Enhancers	Esophagus	oesophagus
15	chr15:79043000-79043800	Enhancers	Thymus	Thymus
16	chr15:79043000-79044000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr15:79043000-79044000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr15:79043000-79044000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr15:79043000-79044000	Enhancers	Left Ventricle	heart
20	chr15:79043000-79044000	Enhancers	Stomach Mucosa	stomach
21	chr15:79043000-79044000	Enhancers	HUVEC	blood vessel
22	chr15:79043000-79044200	Enhancers	Primary B cells from peripheral blood	blood
23	chr15:79043000-79044200	Enhancers	Placenta	Placenta
24	chr15:79043000-79044400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr15:79043200-79043800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr15:79043200-79043800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr15:79043200-79043800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:79043200-79043800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:79043200-79043800	Active TSS	Brain Anterior Caudate	brain
30	chr15:79043200-79043800	Enhancers	Lung	lung
31	chr15:79043200-79043800	Active TSS	Rectal Smooth Muscle	rectum
32	chr15:79043200-79044000	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr15:79043200-79044200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:79043200-79044200	Enhancers	Fetal Thymus	thymus
35	chr15:79043200-79044800	Weak transcription	Fetal Brain Male	brain
36	chr15:79043200-79047200	Weak transcription	NHDF-Ad	bronchial
37	chr15:79043400-79043800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:79043400-79043800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:79043400-79043800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:79043400-79043800	Enhancers	Adipose Nuclei	Adipose
41	chr15:79043400-79043800	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr15:79043400-79044000	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr15:79043400-79044000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr15:79043400-79044000	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr15:79043400-79044000	Enhancers	Brain Hippocampus Middle	brain
46	chr15:79043400-79044000	Enhancers	Spleen	Spleen
47	chr15:79043400-79044200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr15:79043400-79044200	Enhancers	Stomach Smooth Muscle	stomach
49	chr15:79043400-79044600	Enhancers	Fetal Muscle Leg	muscle
50	chr15:79043400-79045400	Weak transcription	Right Atrium	heart

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