Variant report

Variant	rs187769789
Chromosome Location	chr15:83477966-83477967
allele	G/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	E2F4	chr15:83477905-83478613	MCF10A-Er-Src	breast:	n/a	chr15:83478321-83478330 chr15:83478439-83478448
2	SP4	chr15:83477932-83478456	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP2	chr15:83477945-83478550	HepG2	liver:	n/a	chr15:83478322-83478332 chr15:83478242-83478252
4	KAP1	chr15:83477258-83478633	HEK293	kidney:	n/a	n/a
5	SP2	chr15:83477961-83478574	H1-hESC	embryonic stem cell:	n/a	chr15:83478322-83478332 chr15:83478242-83478252
6	PML	chr15:83477963-83478744	MCF-7	breast:	n/a	n/a
7	POLR2A	chr15:83477916-83479343	PANC-1	pancreas:	n/a	n/a
8	RFX5	chr15:83477087-83479037	SK-N-SH	brain:	n/a	chr15:83478322-83478331
9	SP1	chr15:83477950-83478531	GM12878	blood:	n/a	chr15:83478320-83478341 chr15:83478233-83478254
10	IRF1	chr15:83477954-83478608	K562	blood:	n/a	chr15:83478369-83478382 chr15:83478368-83478382 chr15:83478321-83478330 chr15:83478369-83478383 chr15:83478368-83478382
11	TAF1	chr15:83477948-83478810	ECC-1	luminal epithelium:	n/a	n/a
12	SMC3	chr15:83477755-83478357	HepG2	liver:	n/a	n/a
13	SP1	chr15:83477963-83478556	H1-hESC	embryonic stem cell:	n/a	chr15:83478320-83478341 chr15:83478233-83478254
14	MYBL2	chr15:83477830-83478669	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr15:83477713-83478802	MCF-7	breast:	n/a	n/a
16	E2F6	chr15:83477903-83478761	A549	lung:	n/a	chr15:83478321-83478330 chr15:83478439-83478448
17	PBX3	chr15:83477929-83478656	A549	lung:	n/a	chr15:83478322-83478331
18	RELA	chr15:83477637-83478640	GM19099	blood:	n/a	n/a
19	POLR2A	chr15:83477963-83479741	GM19099	blood:	n/a	n/a
20	SIX5	chr15:83477921-83478657	A549	lung:	n/a	n/a
21	POLR2A	chr15:83477789-83479413	GM18951	blood:	n/a	n/a
22	POLR2A	chr15:83477916-83478625	SK-N-SH	brain:	n/a	n/a
23	CEBPB	chr15:83477904-83478473	MCF-7	breast:	n/a	chr15:83478322-83478330
24	NFYA	chr15:83477917-83478539	GM12878	blood:	n/a	chr15:83478319-83478334 chr15:83478319-83478332 chr15:83478319-83478333 chr15:83478319-83478334 chr15:83478321-83478331 chr15:83478236-83478254 chr15:83478241-83478255
25	POLR2A	chr15:83477925-83478668	HCT-116	colon:	n/a	n/a
26	RCOR1	chr15:83477120-83479262	K562	blood:	n/a	n/a
27	MAX	chr15:83477923-83479170	K562	blood:	n/a	n/a
28	NR2F2	chr15:83477886-83478625	K562	blood:	n/a	n/a
29	SP1	chr15:83477856-83478656	HCT-116	colon:	n/a	chr15:83478320-83478341 chr15:83478233-83478254
30	TBP	chr15:83477923-83478575	Hela-S3	cervix:	n/a	n/a
31	BHLHE40	chr15:83477856-83479095	GM12878	blood:	n/a	n/a
32	POLR2A	chr15:83477429-83479340	GM15510	blood:	n/a	n/a
33	SIN3AK20	chr15:83477900-83478307	HepG2	liver:	n/a	n/a
34	RFX5	chr15:83477901-83478590	GM12878	blood:	n/a	chr15:83478322-83478331
35	HCFC1	chr15:83477536-83480275	Hela-S3	cervix:	n/a	n/a
36	MAFK	chr15:83477833-83478138	HepG2	liver:	n/a	n/a
37	ZNF143	chr15:83477895-83478609	Hela-S3	cervix:	n/a	chr15:83478438-83478448 chr15:83478180-83478199
38	KAP1	chr15:83477330-83478610	U2OS	brain:	n/a	n/a
39	NFYB	chr15:83477803-83478710	GM12878	blood:	n/a	chr15:83478319-83478334 chr15:83478319-83478332 chr15:83478319-83478333 chr15:83478319-83478334 chr15:83478321-83478331 chr15:83478242-83478257 chr15:83478241-83478255
40	MAX	chr15:83477932-83479191	A549	lung:	n/a	n/a
41	TBL1XR1	chr15:83477966-83478677	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:83477567-83478690	HEK293	kidney:	n/a	n/a
43	POLR2A	chr15:83477951-83480455	GM12878	blood:	n/a	n/a
44	POLR2A	chr15:83477132-83479406	GM12892	blood:	n/a	n/a
45	MAX	chr15:83477941-83479340	GM12878	blood:	n/a	n/a
46	MAFK	chr15:83477816-83478596	K562	blood:	n/a	n/a
47	REST	chr15:83477947-83478949	H1-neurons	neurons:	n/a	chr15:83478342-83478356 chr15:83478344-83478354 chr15:83478307-83478320 chr15:83478419-83478432
48	RCOR1	chr15:83477907-83478672	GM12878	blood:	n/a	n/a
49	SP1	chr15:83477819-83478601	HCT-116	colon:	n/a	chr15:83478320-83478341 chr15:83478233-83478254
50	GTF2F1	chr15:83477671-83478577	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:83477965-83478015	AG10803	skin:	n/a
2	chr15:83477965-83478015	GM12878	blood:	n/a
3	chr15:83477965-83478015	ovcar-3	ovarian:	n/a
4	chr15:83477965-83478015	LNCaP	prostate:	n/a
5	chr15:83477965-83478015	T-47D	breast:	n/a
6	chr15:83477965-83478015	K562	blood:	n/a
7	chr15:83477965-83478015	BE2_C	brain:	n/a
8	chr15:83477965-83478015	Hela-S3	cervix:	n/a
9	chr15:83477965-83478015	HCF	heart:	n/a
10	chr15:83477965-83478015	HRCEpiC	kidney:	n/a
11	chr15:83477965-83478015	NH-A	brain:	n/a
12	chr15:83477965-83478015	HepG2	liver:	n/a
13	chr15:83477965-83478015	NT2-D1	testis:	n/a
14	chr15:83477965-83478015	HAEpiC	amniotic membrane:	n/a
15	chr15:83477965-83478015	GM12891	blood:	n/a
16	chr15:83477965-83478015	AG09319	gingival:	n/a
17	chr15:83477965-83478015	SKMC	muscle:	n/a
18	chr15:83477965-83478015	HCT-116	colon:	n/a
19	chr15:83477965-83478015	HRPEpiC	eye:	n/a
20	chr15:83477965-83478015	HCPEpiC	choroid plexus:	n/a
21	chr15:83477965-83478015	NHBE	bronchial:	n/a
22	chr15:83477965-83478015	HIPEpiC	eye:	n/a
23	chr15:83477965-83478015	HEK293	kidney:	embryo
24	chr15:83477965-83478015	HCM	heart:	n/a
25	chr15:83477965-83478015	NB4	blood:	n/a
26	chr15:83477965-83478015	HMEC	breast:	n/a
27	chr15:83477965-83478015	IMR90	lung:	fetal
28	chr15:83477965-83478015	Hepatocyte	liver:	n/a
29	chr15:83477965-83478015	ProgFib	skin:	n/a
30	chr15:83477965-83478015	HUVEC	blood vessel:	n/a
31	chr15:83477965-83478015	HPAEpiC	pulmonary alveolar:	n/a
32	chr15:83477965-83478015	AoSMC	blood vessel:	n/a
33	chr15:83477965-83478015	MCF-7	breast:	n/a
34	chr15:83477965-83478015	SK-N-SH_RA	brain:	n/a
35	chr15:83477965-83478015	AG04450	lung:	fetal
36	chr15:83477965-83478015	PANC-1	pancreas:	n/a
37	chr15:83477965-83478015	SK-N-MC	brain:	n/a
38	chr15:83477965-83478015	ECC-1	luminal epithelium:	n/a
39	chr15:83477965-83478015	SAEC	small airway:	n/a
40	chr15:83477965-83478015	SK-N-SH	brain:	n/a
41	chr15:83477965-83478015	PFSK-1	brain:	n/a
42	chr15:83477965-83478015	BJ	skin:	n/a
43	chr15:83477965-83478015	HNPCEpiC	eye:	n/a
44	chr15:83477965-83478015	RPTEC	kidney:	n/a
45	chr15:83477965-83478015	MCF10A-Er-Src	breast:	n/a
46	chr15:83477965-83478015	AG04449	skin:	fetal
47	chr15:83477965-83478015	Caco-2	colon:	n/a
48	chr15:83477965-83478015	HEEpiC	esophagus:	n/a
49	chr15:83477965-83478015	U87	brain:	n/a
50	chr15:83477965-83478015	PrEC	prostate:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:83423255..83426158-chr15:83477607..83479598,3	MCF-7	breast:
2	chr15:83475882..83480852-chr15:83678880..83683242,6	MCF-7	breast:
3	chr15:83477828..83481866-chr15:83483118..83489176,7	K562	blood:
4	chr15:83313427..83317808-chr15:83477553..83483000,6	K562	blood:
5	chr15:83407361..83409606-chr15:83477408..83479472,2	MCF-7	breast:
6	chr15:83417500..83421911-chr15:83474614..83480217,8	MCF-7	breast:
7	chr15:83476033..83478214-chr15:83679893..83681510,2	K562	blood:
8	chr15:83417832..83422548-chr15:83476028..83480956,9	K562	blood:
9	chr15:83477527..83479377-chr15:83517237..83519936,2	K562	blood:
10	chr15:83476923..83480237-chr15:83875108..83878990,4	MCF-7	breast:
11	chr15:83477632..83480172-chr15:83484528..83487051,2	MCF-7	breast:
12	chr15:83477529..83479377-chr15:83517237..83520056,3	K562	blood:
13	chr15:83477554..83479674-chr15:83486165..83489315,3	MCF-7	breast:
14	chr15:83417361..83424147-chr15:83476165..83481050,26	MCF-7	breast:
15	chr15:83348193..83350766-chr15:83477443..83480779,4	MCF-7	breast:
16	chr15:83417749..83420684-chr15:83476028..83479878,6	K562	blood:

Variant related genes	Relation type
WHAMM	TF binding region
FSD2	TF binding region
WHAMM	CpG island
FSD2	CpG island
ENSG00000259462	Chromatin interaction
ENSG00000260608	Chromatin interaction
ENSG00000259315	Chromatin interaction
ENSG00000250988	Chromatin interaction
ENSG00000252690	Chromatin interaction
ENSG00000103723	Chromatin interaction
ENSG00000214575	Chromatin interaction
ENSG00000156232	Chromatin interaction
ENSG00000166503	Chromatin interaction
ENSG00000103942	Chromatin interaction
ENSG00000169609	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS 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
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	esv3371602	chr15:83476798-83481096	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83471200-83478200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:83472400-83478200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:83475000-83478400	Weak transcription	Left Ventricle	heart
4	chr15:83475600-83478000	Enhancers	Fetal Muscle Leg	muscle
5	chr15:83477000-83478000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr15:83477200-83478000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:83477200-83478000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr15:83477200-83478200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr15:83477400-83478000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:83477400-83478000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr15:83477400-83478000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:83477400-83478000	Enhancers	Primary hematopoietic stem cells	blood
13	chr15:83477400-83478000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr15:83477400-83478000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr15:83477400-83478000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr15:83477400-83478000	Enhancers	Fetal Intestine Small	intestine
17	chr15:83477400-83478000	Enhancers	Fetal Muscle Trunk	muscle
18	chr15:83477400-83478000	Enhancers	Lung	lung
19	chr15:83477400-83478000	Enhancers	Pancreas	Pancrea
20	chr15:83477400-83478000	Enhancers	Thymus	Thymus
21	chr15:83477400-83478000	Enhancers	HMEC	breast
22	chr15:83477400-83478000	Enhancers	HSMM	muscle
23	chr15:83477400-83478200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:83477400-83478200	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr15:83477400-83478200	Flanking Active TSS	Fetal Heart	heart
26	chr15:83477400-83478200	Flanking Active TSS	Dnd41	blood
27	chr15:83477400-83478200	Flanking Active TSS	GM12878-XiMat	blood
28	chr15:83477400-83478200	Flanking Active TSS	Hela-S3	cervix
29	chr15:83477400-83478200	Flanking Active TSS	K562	blood
30	chr15:83477400-83480400	Active TSS	Colonic Mucosa	Colon
31	chr15:83477400-83480400	Active TSS	Stomach Mucosa	stomach
32	chr15:83477400-83481000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:83477600-83478000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:83477600-83478000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr15:83477600-83478000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:83477600-83478000	Enhancers	Fetal Lung	lung
37	chr15:83477600-83478000	Enhancers	Fetal Stomach	stomach
38	chr15:83477600-83478200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr15:83477600-83478200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:83477600-83478200	Enhancers	Spleen	Spleen
41	chr15:83477600-83478200	Flanking Active TSS	A549	lung
42	chr15:83477600-83479600	Active TSS	Brain Anterior Caudate	brain
43	chr15:83477600-83480200	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr15:83477600-83480400	Active TSS	Psoas Muscle	Psoas
45	chr15:83477600-83480800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:83477800-83478000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:83477800-83478000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:83477800-83478000	Enhancers	Primary T cells from cord blood	blood
49	chr15:83477800-83478000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:83477800-83478000	Flanking Active TSS	Brain Hippocampus Middle	brain

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