Variant report

Variant	rs73398510
Chromosome Location	chr15:41056114-41056115
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	POLR2A	chr15:41055928-41057125	GM12891	blood:	n/a	n/a
2	E2F6	chr15:41056029-41056513	H1-hESC	embryonic stem cell:	n/a	chr15:41056207-41056216
3	PAX5	chr15:41056054-41056526	GM12878	blood:	n/a	n/a
4	HEY1	chr15:41055302-41056572	HepG2	liver:	n/a	chr15:41055499-41055514
5	E2F6	chr15:41056052-41056481	A549	lung:	n/a	chr15:41056207-41056216
6	YY1	chr15:41056008-41056477	GM12892	blood:	n/a	chr15:41056192-41056203
7	HEY1	chr15:41055808-41056524	K562	blood:	n/a	n/a
8	POLR2A	chr15:41055920-41056820	GM19193	blood:	n/a	n/a
9	RFX5	chr15:41055334-41056939	Hela-S3	cervix:	n/a	chr15:41055483-41055497
10	POLR2A	chr15:41055349-41059478	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr15:41055852-41056659	HepG2	liver:	n/a	n/a
12	HCFC1	chr15:41055962-41056647	K562	blood:	n/a	n/a
13	ZNF143	chr15:41056114-41056654	Hela-S3	cervix:	n/a	n/a
14	GABPA	chr15:41055993-41056849	K562	blood:	n/a	n/a
15	E2F1	chr15:41055371-41056714	Hela-S3	cervix:	n/a	chr15:41056207-41056216 chr15:41055940-41055949 chr15:41055502-41055511 chr15:41056701-41056713
16	CTCF	chr15:41056040-41056647	H1-hESC	embryonic stem cell:	n/a	chr15:41056060-41056073 chr15:41056345-41056354
17	CTCF	chr15:41055918-41056531	A549	lung:	n/a	chr15:41056060-41056073 chr15:41056345-41056354
18	CTCF	chr15:41056063-41056494	K562	blood:	n/a	chr15:41056345-41056354
19	ARID3A	chr15:41055966-41056143	HepG2	liver:	n/a	n/a
20	NFIC	chr15:41055278-41056184	HepG2	liver:	n/a	chr15:41055583-41055599 chr15:41055582-41055599 chr15:41055581-41055598
21	UBTF	chr15:41055478-41056937	K562	blood:	n/a	n/a
22	MAX	chr15:41056079-41056655	NB4	blood:	n/a	n/a
23	YY1	chr15:41056094-41056581	ECC-1	luminal epithelium:	n/a	chr15:41056192-41056203
24	POLR2A	chr15:41055417-41056733	HepG2	liver:	n/a	n/a
25	ZBTB7A	chr15:41055540-41056828	ECC-1	luminal epithelium:	n/a	n/a
26	NFYB	chr15:41055883-41056626	Hela-S3	cervix:	n/a	chr15:41056203-41056218 chr15:41056203-41056218 chr15:41056206-41056216 chr15:41056205-41056220
27	POLR2A	chr15:41055937-41056687	MCF10A-Er-Src	breast:	n/a	n/a
28	TAF1	chr15:41055959-41056458	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr15:41056044-41056821	GM12878	blood:	n/a	n/a
30	MAX	chr15:41055194-41056853	HepG2	liver:	n/a	chr15:41056062-41056072 chr15:41055747-41055757
31	TFAP2A	chr15:41055325-41057035	Hela-S3	cervix:	n/a	chr15:41056124-41056132 chr15:41056124-41056132 chr15:41055719-41055731 chr15:41056124-41056132
32	CTCF	chr15:41056021-41056452	K562	blood:	n/a	chr15:41056060-41056073 chr15:41056345-41056354
33	CHD2	chr15:41056089-41056683	H1-hESC	embryonic stem cell:	n/a	n/a
34	E2F4	chr15:41055331-41056747	K562	blood:	n/a	chr15:41056207-41056216 chr15:41055940-41055949 chr15:41055502-41055511 chr15:41055526-41055537 chr15:41056701-41056713
35	POLR2A	chr15:41055827-41056644	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr15:41055791-41056714	HepG2	liver:	n/a	n/a
37	CTCF	chr15:41056078-41056457	GM12878	blood:	n/a	chr15:41056345-41056354
38	NFYA	chr15:41055891-41056759	Hela-S3	cervix:	n/a	chr15:41056203-41056218 chr15:41056199-41056217 chr15:41056203-41056218 chr15:41056206-41056216
39	CBX3	chr15:41055232-41056593	K562	blood:	n/a	n/a
40	CHD2	chr15:41055906-41056527	HepG2	liver:	n/a	n/a
41	POLR2A	chr15:41055876-41056515	GM12892	blood:	n/a	n/a
42	CREB1	chr15:41055314-41056830	HepG2	liver:	n/a	n/a
43	TCF7L2	chr15:41055549-41056283	PANC-1	pancreas:	n/a	n/a
44	SIN3AK20	chr15:41055293-41056904	MCF-7	breast:	n/a	n/a
45	ELF1	chr15:41055434-41056906	MCF-7	breast:	n/a	chr15:41056583-41056592 chr15:41056679-41056688 chr15:41056678-41056687
46	MAX	chr15:41055326-41056608	H1-hESC	embryonic stem cell:	n/a	chr15:41056062-41056072 chr15:41055747-41055757
47	TAF1	chr15:41055785-41056791	HepG2	liver:	n/a	n/a
48	CTCF	chr15:41056100-41056250	HFF-Myc	foreskin:	n/a	n/a
49	SP1	chr15:41055938-41056529	A549	lung:	n/a	chr15:41056063-41056077 chr15:41056196-41056217
50	RCOR1	chr15:41055246-41056788	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:41056075-41056125	BJ	skin:	n/a
2	chr15:41056075-41056125	PrEC	prostate:	n/a
3	chr15:41056075-41056125	HRE	kidney:	n/a
4	chr15:41056075-41056125	A549	lung:	n/a
5	chr15:41056075-41056125	HUVEC	blood vessel:	n/a
6	chr15:41056075-41056125	MCF-7	breast:	n/a
7	chr15:41056075-41056125	HEEpiC	esophagus:	n/a
8	chr15:41056075-41056125	CMK	blood:	n/a
9	chr15:41056075-41056125	HIPEpiC	eye:	n/a
10	chr15:41056075-41056125	AG04449	skin:	fetal
11	chr15:41056075-41056125	SK-N-SH	brain:	n/a
12	chr15:41056075-41056125	AG10803	skin:	n/a
13	chr15:41056075-41056125	BE2_C	brain:	n/a
14	chr15:41056075-41056125	Hela-S3	cervix:	n/a
15	chr15:41056075-41056125	HPAEpiC	pulmonary alveolar:	n/a
16	chr15:41056075-41056125	Caco-2	colon:	n/a
17	chr15:41056075-41056125	Jurkat	blood:	n/a
18	chr15:41056075-41056125	SKMC	muscle:	n/a
19	chr15:41056075-41056125	HepG2	liver:	n/a
20	chr15:41056075-41056125	PFSK-1	brain:	n/a
21	chr15:41056075-41056125	AG04450	lung:	fetal
22	chr15:41056075-41056125	AG09309	skin:	n/a
23	chr15:41056075-41056125	AoSMC	blood vessel:	n/a
24	chr15:41056075-41056125	NT2-D1	testis:	n/a
25	chr15:41056075-41056125	T-47D	breast:	n/a
26	chr15:41056075-41056125	GM12878	blood:	n/a
27	chr15:41056075-41056125	ECC-1	luminal epithelium:	n/a
28	chr15:41056075-41056125	NB4	blood:	n/a
29	chr15:41056075-41056125	HEK293	kidney:	embryo
30	chr15:41056075-41056125	HCM	heart:	n/a
31	chr15:41056075-41056125	NHDF-neo	bronchial:	n/a
32	chr15:41056075-41056125	NHBE	bronchial:	n/a
33	chr15:41056075-41056125	ovcar-3	ovarian:	n/a
34	chr15:41056075-41056125	RPTEC	kidney:	n/a
35	chr15:41056075-41056125	HRPEpiC	eye:	n/a
36	chr15:41056075-41056125	HNPCEpiC	eye:	n/a
37	chr15:41056075-41056125	K562	blood:	n/a
38	chr15:41056075-41056125	HRCEpiC	kidney:	n/a
39	chr15:41056075-41056125	H1-hESC	embryonic stem cell:	embryo
40	chr15:41056075-41056125	HMEC	breast:	n/a
41	chr15:41056075-41056125	SAEC	small airway:	n/a
42	chr15:41056075-41056125	Hepatocyte	liver:	n/a
43	chr15:41056075-41056125	MCF10A-Er-Src	breast:	n/a
44	chr15:41056075-41056125	LNCaP	prostate:	n/a
45	chr15:41056075-41056125	GM06990	blood:	n/a
46	chr15:41056075-41056125	AG09319	gingival:	n/a
47	chr15:41056075-41056125	GM12892	blood:	n/a
48	chr15:41056075-41056125	PANC-1	pancreas:	n/a
49	chr15:41056075-41056125	HCPEpiC	choroid plexus:	n/a
50	chr15:41056075-41056125	NH-A	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40990811..40992810-chr15:41055825..41057654,2	MCF-7	breast:
2	chr15:41053870..41057648-chr15:41097391..41099914,3	K562	blood:
3	chr15:41055462..41056415-chr15:72977930..72978582,2	Hela-S3	cervix:
4	chr15:41042059..41049706-chr15:41053861..41061949,15	MCF-7	breast:
5	chr15:40985800..40990095-chr15:41055400..41057901,4	K562	blood:
6	chr15:41055895..41056540-chr7:66767078..66768033,2	Hela-S3	cervix:
7	chr15:41056057..41057921-chr15:41407305..41409021,2	K562	blood:
8	chr12:120729277..120729973-chr15:41055717..41056485,2	Hela-S3	cervix:
9	chr15:41054213..41057951-chr15:41097645..41100150,5	K562	blood:
10	chr15:41053928..41056375-chr15:41057436..41059478,2	MCF-7	breast:
11	chr15:41056057..41058777-chr15:41406413..41409021,2	K562	blood:
12	chr15:41055458..41058081-chr15:41065711..41068133,2	K562	blood:
13	chr15:41054628..41058503-chr15:41058814..41065530,15	K562	blood:
14	chr1:45186932..45187822-chr15:41055556..41056385,2	Hela-S3	cervix:
15	chr15:41036948..41038953-chr15:41054723..41057087,2	K562	blood:
16	chr15:41055716..41060288-chr15:41072655..41077591,4	MCF-7	breast:

Variant related genes	Relation type
GCHFR	TF binding region
GCHFR	CpG island
ENSG00000137880	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000188277	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000067601	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000106610	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000175202	Chromatin interaction
ENSG00000140463	Chromatin interaction
ENSG00000245849	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16971013	0.83[AMR][1000 genomes]
rs16971015	0.83[AMR][1000 genomes]
rs2004043	0.83[AMR][1000 genomes]
rs2412552	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28480346	0.83[AMR][1000 genomes]
rs28498351	0.83[AMR][1000 genomes]
rs28718778	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58036350	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61317135	0.83[AMR][1000 genomes]
rs6492966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7165694	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7172251	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7182456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73398512	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73398517	0.80[AFR][1000 genomes]
rs73398522	0.80[AFR][1000 genomes]
rs934783	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41054800-41056600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:41055000-41057000	Bivalent Enhancer	Fetal Brain Male	brain
3	chr15:41055200-41056400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
4	chr15:41055200-41056800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:41055200-41057200	Flanking Active TSS	Placenta	Placenta
6	chr15:41055200-41057200	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr15:41055200-41057600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:41055200-41058000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr15:41055400-41056200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr15:41055400-41056200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:41055400-41056200	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr15:41055400-41056200	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr15:41055400-41056200	Flanking Active TSS	Stomach Mucosa	stomach
14	chr15:41055400-41056400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:41055400-41056600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:41055400-41056600	Flanking Active TSS	Pancreas	Pancrea
17	chr15:41055400-41056600	Flanking Active TSS	Right Ventricle	heart
18	chr15:41055400-41056800	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr15:41055400-41056800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr15:41055400-41056800	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr15:41055400-41056800	Flanking Active TSS	HUVEC	blood vessel
22	chr15:41055400-41057000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:41055400-41057000	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr15:41055400-41057000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr15:41055400-41057000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:41055400-41057000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:41055400-41057000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:41055400-41057000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
29	chr15:41055400-41057000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr15:41055400-41057000	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr15:41055400-41057000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
32	chr15:41055400-41057000	Flanking Active TSS	NH-A	brain
33	chr15:41055400-41057200	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr15:41055400-41057200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:41055400-41057200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr15:41055400-41057200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:41055400-41057200	Flanking Active TSS	Colonic Mucosa	Colon
38	chr15:41055400-41057200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr15:41055400-41057200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr15:41055400-41057400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr15:41055400-41057400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr15:41055400-41057400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:41055400-41057400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr15:41055400-41057600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:41055400-41057600	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr15:41055400-41057600	Flanking Active TSS	Osteobl	bone
47	chr15:41055400-41058000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr15:41055400-41058000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:41055400-41058000	Flanking Active TSS	NHEK	skin
50	chr15:41055600-41056200	Flanking Active TSS	Fetal Heart	heart

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