Variant report

Variant	rs4887091
Chromosome Location	chr15:79043580-79043581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:280)
CpG islands
(count:61)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:280 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:79043520-79043670	AG04450	lung:	n/a	n/a
2	EBF1	chr15:79043315-79043645	GM12878	blood:	n/a	n/a
3	CTCF	chr15:79043394-79043777	H1-hESC	embryonic stem cell:	n/a	chr15:79043461-79043474
4	SMC3	chr15:79043388-79043760	K562	blood:	n/a	n/a
5	CTCF	chr15:79043444-79043727	Kidney_OC	kidney:	n/a	chr15:79043461-79043474
6	CTCF	chr15:79043434-79043715	LNCaP	prostate:	n/a	chr15:79043461-79043474
7	CTCF	chr15:79043500-79043650	K562	blood:	n/a	n/a
8	CHD2	chr15:79043464-79043664	GM12878	blood:	n/a	n/a
9	CTCF	chr15:79043500-79043650	WI-38	lung:	n/a	n/a
10	RAD21	chr15:79043354-79043732	SK-N-SH_RA	brain:	n/a	n/a
11	CTCF	chr15:79043290-79043827	MCF-7	breast:	n/a	chr15:79043461-79043474
12	CTCF	chr15:79043520-79043670	GM12866	blood:	n/a	n/a
13	FOXP2	chr15:79043493-79043673	SK-N-MC	brain:	n/a	n/a
14	TBL1XR1	chr15:79043571-79043633	K562	blood:	n/a	n/a
15	RAD21	chr15:79043392-79043754	A549	lung:	n/a	n/a
16	HCFC1	chr15:79043059-79043907	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr15:79043398-79043668	HepG2	liver:	n/a	chr15:79043461-79043474
18	GTF2F1	chr15:79043332-79043670	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr15:79043540-79043690	GM12872	blood:	n/a	n/a
20	MAZ	chr15:79043403-79043722	GM12878	blood:	n/a	chr15:79043538-79043548
21	CTCF	chr15:79043480-79043630	BJ	skin:	n/a	n/a
22	CTCF	chr15:79043520-79043670	HVMF	connective:	n/a	n/a
23	CTCF	chr15:79043424-79043715	A549	lung:	n/a	chr15:79043461-79043474
24	EP300	chr15:79043557-79043707	K562	blood:	n/a	n/a
25	CTCF	chr15:79043560-79043710	HCM	heart:	n/a	n/a
26	CREB1	chr15:79043426-79043691	A549	lung:	n/a	n/a
27	CTCF	chr15:79043451-79043689	HepG2	liver:	n/a	chr15:79043461-79043474
28	POU2F2	chr15:79043410-79043683	GM12878	blood:	n/a	n/a
29	SMC3	chr15:79043410-79043760	GM12878	blood:	n/a	n/a
30	YY1	chr15:79043411-79043720	GM12878	blood:	n/a	n/a
31	TBP	chr15:79043406-79043600	Hela-S3	cervix:	n/a	n/a
32	ZMIZ1	chr15:79043561-79043633	K562	blood:	n/a	n/a
33	CTCF	chr15:79043500-79043650	BJ	skin:	n/a	n/a
34	CTCF	chr15:79043420-79043750	Lung_OC	lung:	n/a	chr15:79043461-79043474
35	CTCF	chr15:79043540-79043690	NHDF-neo	bronchial:	n/a	n/a
36	CTCF	chr15:79043500-79043650	HMF	breast:	n/a	n/a
37	CTCF	chr15:79043520-79043670	GM12871	blood:	n/a	n/a
38	CTCF	chr15:79043441-79043769	HepG2	liver:	n/a	chr15:79043461-79043474
39	CTCF	chr15:79043394-79043745	GM19239	blood:	n/a	chr15:79043461-79043474
40	CTCF	chr15:79043459-79043709	GM10248	blood:	n/a	chr15:79043461-79043474
41	TEAD4	chr15:79043349-79043774	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr15:79043402-79043894	GM19238	blood:	n/a	chr15:79043461-79043474
43	STAT1	chr15:79043450-79043657	GM12878	blood:	n/a	n/a
44	POLR2A	chr15:79043169-79043637	U87	brain:	n/a	n/a
45	TCF3	chr15:79043361-79043673	GM12878	blood:	n/a	chr15:79043646-79043655 chr15:79043643-79043659
46	CTCF	chr15:79043392-79043727	NHEK	skin:	n/a	chr15:79043461-79043474
47	CTCF	chr15:79043500-79043650	NHEK	skin:	n/a	n/a
48	ZNF384	chr15:79043482-79043636	K562	blood:	n/a	n/a
49	EGR1	chr15:79043410-79043628	GM12878	blood:	n/a	chr15:79043478-79043492 chr15:79043479-79043493 chr15:79043480-79043490 chr15:79043477-79043492 chr15:79043537-79043551 chr15:79043502-79043516
50	CTCF	chr15:79043441-79043724	GM10266	blood:	n/a	chr15:79043461-79043474

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:79043531-79043581	HIPEpiC	eye:	n/a
2	chr15:79043531-79043581	PANC-1	pancreas:	n/a
3	chr15:79043531-79043581	HUVEC	blood vessel:	n/a
4	chr15:79043531-79043581	ovcar-3	ovarian:	n/a
5	chr15:79043531-79043581	NHBE	bronchial:	n/a
6	chr15:79043531-79043581	GM12892	blood:	n/a
7	chr15:79043531-79043581	T-47D	breast:	n/a
8	chr15:79043531-79043581	MCF10A-Er-Src	breast:	n/a
9	chr15:79043531-79043581	HCT-116	colon:	n/a
10	chr15:79043531-79043581	SKMC	muscle:	n/a
11	chr15:79043531-79043581	SK-N-SH_RA	brain:	n/a
12	chr15:79043531-79043581	ECC-1	luminal epithelium:	n/a
13	chr15:79043531-79043581	HAEpiC	amniotic membrane:	n/a
14	chr15:79043531-79043581	AG09309	skin:	n/a
15	chr15:79043531-79043581	SAEC	small airway:	n/a
16	chr15:79043531-79043581	AG09319	gingival:	n/a
17	chr15:79043531-79043581	GM19239	blood:	n/a
18	chr15:79043531-79043581	HCF	heart:	n/a
19	chr15:79043531-79043581	GM06990	blood:	n/a
20	chr15:79043531-79043581	AoSMC	blood vessel:	n/a
21	chr15:79043531-79043581	HCPEpiC	choroid plexus:	n/a
22	chr15:79043531-79043581	CMK	blood:	n/a
23	chr15:79043531-79043581	Hela-S3	cervix:	n/a
24	chr15:79043531-79043581	BJ	skin:	n/a
25	chr15:79043531-79043581	BE2_C	brain:	n/a
26	chr15:79043531-79043581	MCF-7	breast:	n/a
27	chr15:79043531-79043581	NHDF-neo	bronchial:	n/a
28	chr15:79043531-79043581	RPTEC	kidney:	n/a
29	chr15:79043531-79043581	AG04449	skin:	fetal
30	chr15:79043531-79043581	NH-A	brain:	n/a
31	chr15:79043531-79043581	HepG2	liver:	n/a
32	chr15:79043531-79043581	AG10803	skin:	n/a
33	chr15:79043531-79043581	PrEC	prostate:	n/a
34	chr15:79043531-79043581	PFSK-1	brain:	n/a
35	chr15:79043531-79043581	ProgFib	skin:	n/a
36	chr15:79043531-79043581	HMEC	breast:	n/a
37	chr15:79043531-79043581	HRCEpiC	kidney:	n/a
38	chr15:79043531-79043581	SK-N-SH	brain:	n/a
39	chr15:79043531-79043581	HCM	heart:	n/a
40	chr15:79043531-79043581	Caco-2	colon:	n/a
41	chr15:79043531-79043581	U87	brain:	n/a
42	chr15:79043531-79043581	K562	blood:	n/a
43	chr15:79043531-79043581	SK-N-MC	brain:	n/a
44	chr15:79043531-79043581	AG04450	lung:	fetal
45	chr15:79043531-79043581	HNPCEpiC	eye:	n/a
46	chr15:79043531-79043581	HRE	kidney:	n/a
47	chr15:79043531-79043581	H1-hESC	embryonic stem cell:	embryo
48	chr15:79043531-79043581	HL-60	blood:	n/a
49	chr15:79043531-79043581	GM12878	blood:	n/a
50	chr15:79043531-79043581	HRPEpiC	eye:	n/a

(count:13 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11072787	0.85[CEU][hapmap]
rs11072800	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899201	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12899940	0.94[CEU][hapmap]
rs12901228	0.81[ASN][1000 genomes]
rs12904489	0.88[AMR][1000 genomes];0.86[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];0.95[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];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907207	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907432	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907536	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12909668	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12910831	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12912245	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12913779	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12917502	0.97[AMR][1000 genomes];0.84[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]
rs1809412	0.94[CEU][hapmap]
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];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2017297	0.82[AMR][1000 genomes];0.83[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];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34019568	0.81[ASN][1000 genomes]
rs3861181	0.80[CEU][hapmap]
rs4886982	1.00[JPT][hapmap]
rs4887074	0.80[CEU][hapmap]
rs4887078	0.95[CEU][hapmap]
rs4887092	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	0.84[EUR][1000 genomes]
rs7177143	0.85[ASN][1000 genomes]
rs7182567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182694	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182993	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755998	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8024939	0.85[ASN][1000 genomes]
rs8030090	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8030335	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs899997	0.95[CEU][hapmap]

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:80 , 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	chr15:79043000-79043600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:79043000-79043600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:79043000-79043600	Enhancers	Colonic Mucosa	Colon
13	chr15:79043000-79043600	Active TSS	A549	lung
14	chr15:79043000-79043600	Bivalent/Poised TSS	HepG2	liver
15	chr15:79043000-79043600	Flanking Active TSS	HSMM	muscle
16	chr15:79043000-79043800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr15:79043000-79043800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:79043000-79043800	Active TSS	Colon Smooth Muscle	Colon
19	chr15:79043000-79043800	Enhancers	Duodenum Mucosa	Duodenum
20	chr15:79043000-79043800	Enhancers	Esophagus	oesophagus
21	chr15:79043000-79043800	Enhancers	Thymus	Thymus
22	chr15:79043000-79044000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr15:79043000-79044000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr15:79043000-79044000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr15:79043000-79044000	Enhancers	Left Ventricle	heart
26	chr15:79043000-79044000	Enhancers	Stomach Mucosa	stomach
27	chr15:79043000-79044000	Enhancers	HUVEC	blood vessel
28	chr15:79043000-79044200	Enhancers	Primary B cells from peripheral blood	blood
29	chr15:79043000-79044200	Enhancers	Placenta	Placenta
30	chr15:79043000-79044400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr15:79043200-79043600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:79043200-79043600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:79043200-79043600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:79043200-79043600	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr15:79043200-79043600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:79043200-79043600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:79043200-79043600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:79043200-79043600	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr15:79043200-79043600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr15:79043200-79043600	Active TSS	Ovary	ovary
41	chr15:79043200-79043600	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr15:79043200-79043600	Active TSS	NHEK	skin
43	chr15:79043200-79043600	Active TSS	Osteobl	bone
44	chr15:79043200-79043800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
45	chr15:79043200-79043800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr15:79043200-79043800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:79043200-79043800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:79043200-79043800	Active TSS	Brain Anterior Caudate	brain
49	chr15:79043200-79043800	Enhancers	Lung	lung
50	chr15:79043200-79043800	Active TSS	Rectal Smooth Muscle	rectum

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