Variant report

Variant	rs2412552
Chromosome Location	chr15:41056786-41056787
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:121)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:121 , 50 per page) page: 1 2 3

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	POLR2A	chr15:41055920-41056820	GM19193	blood:	n/a	n/a
3	RFX5	chr15:41055334-41056939	Hela-S3	cervix:	n/a	chr15:41055483-41055497
4	POLR2A	chr15:41055349-41059478	PANC-1	pancreas:	n/a	n/a
5	GABPA	chr15:41055993-41056849	K562	blood:	n/a	n/a
6	UBTF	chr15:41055478-41056937	K562	blood:	n/a	n/a
7	ZBTB7A	chr15:41055540-41056828	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr15:41056044-41056821	GM12878	blood:	n/a	n/a
9	MAX	chr15:41055194-41056853	HepG2	liver:	n/a	chr15:41056062-41056072 chr15:41055747-41055757
10	TFAP2A	chr15:41055325-41057035	Hela-S3	cervix:	n/a	chr15:41056124-41056132 chr15:41056124-41056132 chr15:41055719-41055731 chr15:41056124-41056132
11	MTA3	chr15:41056685-41057308	GM12878	blood:	n/a	n/a
12	CREB1	chr15:41055314-41056830	HepG2	liver:	n/a	n/a
13	SIN3AK20	chr15:41055293-41056904	MCF-7	breast:	n/a	n/a
14	ELF1	chr15:41055434-41056906	MCF-7	breast:	n/a	chr15:41056583-41056592 chr15:41056679-41056688 chr15:41056678-41056687
15	TAF1	chr15:41055785-41056791	HepG2	liver:	n/a	n/a
16	NFIC	chr15:41056286-41056798	GM12878	blood:	n/a	n/a
17	RCOR1	chr15:41055246-41056788	K562	blood:	n/a	n/a
18	POLR2A	chr15:41055879-41057224	Raji	blood:	n/a	n/a
19	POLR2A	chr15:41055321-41057248	HepG2	liver:	n/a	n/a
20	MAX	chr15:41055186-41057114	ECC-1	luminal epithelium:	n/a	chr15:41056062-41056072 chr15:41055747-41055757
21	TFAP2C	chr15:41055288-41057328	Hela-S3	cervix:	n/a	n/a
22	TCF12	chr15:41055258-41056855	ECC-1	luminal epithelium:	n/a	chr15:41055478-41055485
23	ZBTB7A	chr15:41055362-41056908	ECC-1	luminal epithelium:	n/a	n/a
24	TBP	chr15:41055513-41056934	HepG2	liver:	n/a	n/a
25	POLR2A	chr15:41055875-41057352	MCF-7	breast:	n/a	n/a
26	EP300	chr15:41055257-41056943	ECC-1	luminal epithelium:	n/a	chr15:41055940-41055949 chr15:41055990-41056000 chr15:41056929-41056943
27	ZNF263	chr15:41055491-41057061	HEK293-T-REx	kidney:	n/a	chr15:41056066-41056075
28	POLR2A	chr15:41055336-41056929	Hela-S3	cervix:	n/a	n/a
29	MTA3	chr15:41055408-41058034	GM12878	blood:	n/a	n/a
30	MAZ	chr15:41055397-41057030	K562	blood:	n/a	chr15:41056062-41056072 chr15:41055747-41055757
31	POLR2A	chr15:41055940-41056841	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr15:41056745-41057053	HepG2	liver:	n/a	n/a
33	POLR2A	chr15:41055815-41056887	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr15:41055474-41058908	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:41055341-41056831	HL-60	blood:	n/a	n/a
36	MXI1	chr15:41055353-41056829	HepG2	liver:	n/a	n/a
37	POLR2A	chr15:41055973-41059813	K562	blood:	n/a	n/a
38	POLR2A	chr15:41055858-41056795	GM12891	blood:	n/a	n/a
39	SMARCC1	chr15:41055327-41057621	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr15:41055298-41056814	GM12878	blood:	n/a	n/a
41	HA-E2F1	chr15:41055253-41057066	MCF-7	breast:	n/a	chr15:41056207-41056216 chr15:41055940-41055949 chr15:41055502-41055511 chr15:41056701-41056713
42	RUNX3	chr15:41055916-41056959	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:41056044-41056793	NB4	blood:	n/a	n/a
44	CHD2	chr15:41055961-41056843	GM12878	blood:	n/a	n/a
45	MAX	chr15:41056604-41056805	K562	blood:	n/a	n/a
46	GTF2F1	chr15:41055374-41057290	Hela-S3	cervix:	n/a	n/a
47	YY1	chr15:41055330-41056902	HepG2	liver:	n/a	chr15:41056192-41056203
48	HMGN3	chr15:41055402-41056794	K562	blood:	n/a	n/a
49	CHD2	chr15:41055335-41057115	Hela-S3	cervix:	n/a	n/a
50	MAX	chr15:41055321-41057191	Hela-S3	cervix:	n/a	chr15:41056062-41056072 chr15:41055747-41055757

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:41056786-41056836	PFSK-1	brain:	n/a
2	chr15:41056786-41056836	HAEpiC	amniotic membrane:	n/a
3	chr15:41056786-41056836	ECC-1	luminal epithelium:	n/a
4	chr15:41056786-41056836	HCPEpiC	choroid plexus:	n/a
5	chr15:41056786-41056836	U87	brain:	n/a
6	chr15:41056786-41056836	GM12891	blood:	n/a
7	chr15:41056786-41056836	GM19239	blood:	n/a
8	chr15:41056786-41056836	K562	blood:	n/a
9	chr15:41056786-41056836	NH-A	brain:	n/a
10	chr15:41056786-41056836	A549	lung:	n/a
11	chr15:41056786-41056836	HCF	heart:	n/a
12	chr15:41056786-41056836	HEK293	kidney:	embryo
13	chr15:41056786-41056836	NHDF-neo	bronchial:	n/a
14	chr15:41056786-41056836	LNCaP	prostate:	n/a
15	chr15:41056786-41056836	Hela-S3	cervix:	n/a
16	chr15:41056786-41056836	GM12878	blood:	n/a
17	chr15:41056786-41056836	BJ	skin:	n/a
18	chr15:41056786-41056836	HMEC	breast:	n/a
19	chr15:41056786-41056836	IMR90	lung:	fetal
20	chr15:41056786-41056836	HRPEpiC	eye:	n/a
21	chr15:41056786-41056836	RPTEC	kidney:	n/a
22	chr15:41056786-41056836	HRCEpiC	kidney:	n/a
23	chr15:41056786-41056836	HCM	heart:	n/a
24	chr15:41056786-41056836	HepG2	liver:	n/a
25	chr15:41056786-41056836	AoSMC	blood vessel:	n/a
26	chr15:41056786-41056836	GM06990	blood:	n/a
27	chr15:41056786-41056836	SK-N-MC	brain:	n/a
28	chr15:41056786-41056836	AG09309	skin:	n/a
29	chr15:41056786-41056836	NT2-D1	testis:	n/a
30	chr15:41056786-41056836	HUVEC	blood vessel:	n/a
31	chr15:41056786-41056836	H1-hESC	embryonic stem cell:	embryo
32	chr15:41056786-41056836	PrEC	prostate:	n/a
33	chr15:41056786-41056836	PANC-1	pancreas:	n/a
34	chr15:41056786-41056836	AG04450	lung:	fetal
35	chr15:41056786-41056836	NHBE	bronchial:	n/a
36	chr15:41056786-41056836	SAEC	small airway:	n/a
37	chr15:41056786-41056836	HRE	kidney:	n/a
38	chr15:41056786-41056836	NB4	blood:	n/a
39	chr15:41056786-41056836	Hepatocyte	liver:	n/a
40	chr15:41056786-41056836	ProgFib	skin:	n/a
41	chr15:41056786-41056836	AG04449	skin:	fetal
42	chr15:41056786-41056836	HIPEpiC	eye:	n/a
43	chr15:41056786-41056836	HL-60	blood:	n/a
44	chr15:41056786-41056836	MCF-7	breast:	n/a
45	chr15:41056786-41056836	HPAEpiC	pulmonary alveolar:	n/a
46	chr15:41056786-41056836	SK-N-SH_RA	brain:	n/a
47	chr15:41056786-41056836	AG10803	skin:	n/a
48	chr15:41056786-41056836	Caco-2	colon:	n/a
49	chr15:41056786-41056836	T-47D	breast:	n/a
50	chr15:41056786-41056836	HNPCEpiC	eye:	n/a

(count:12 , 50 per page) page: 1

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	chr15:41042059..41049706-chr15:41053861..41061949,15	MCF-7	breast:
4	chr15:40985800..40990095-chr15:41055400..41057901,4	K562	blood:
5	chr15:41056057..41057921-chr15:41407305..41409021,2	K562	blood:
6	chr15:41054213..41057951-chr15:41097645..41100150,5	K562	blood:
7	chr15:41056175..41056885-chr3:196159214..196159919,2	Hela-S3	cervix:
8	chr15:41056057..41058777-chr15:41406413..41409021,2	K562	blood:
9	chr15:41055458..41058081-chr15:41065711..41068133,2	K562	blood:
10	chr15:41054628..41058503-chr15:41058814..41065530,15	K562	blood:
11	chr15:41036948..41038953-chr15:41054723..41057087,2	K562	blood:
12	chr15:41055716..41060288-chr15:41072655..41077591,4	MCF-7	breast:

No data

Variant related genes	Relation type
GCHFR	TF binding region
GCHFR	CpG island
ENSG00000245849	Chromatin interaction
ENSG00000163960	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000188277	Chromatin interaction
ENSG00000104129	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12102251	0.85[AMR][1000 genomes]
rs16970995	0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16970997	0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16971004	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16971008	0.83[AMR][1000 genomes]
rs16971013	1.00[AMR][1000 genomes]
rs16971015	1.00[AMR][1000 genomes]
rs1814415	0.85[AMR][1000 genomes]
rs2004043	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28460049	0.85[AMR][1000 genomes]
rs28480346	1.00[AMR][1000 genomes]
rs28498351	1.00[AMR][1000 genomes]
rs28578011	0.85[AMR][1000 genomes]
rs28716513	0.83[AMR][1000 genomes]
rs28718778	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28727420	0.85[AMR][1000 genomes]
rs28736321	0.85[AMR][1000 genomes]
rs34819163	0.83[AMR][1000 genomes]
rs4343248	0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57191378	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57380807	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58036350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61317135	1.00[AMR][1000 genomes]
rs61405952	0.85[AMR][1000 genomes]
rs6492966	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7165694	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166719	0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7172251	0.83[AMR][1000 genomes]
rs7178363	0.85[AMR][1000 genomes]
rs7182456	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73398510	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73398512	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73398517	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398522	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398528	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398537	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398540	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398560	0.85[AMR][1000 genomes]
rs73398591	0.85[AMR][1000 genomes]
rs934783	1.00[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	chr15:41055000-41057000	Bivalent Enhancer	Fetal Brain Male	brain
2	chr15:41055200-41056800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:41055200-41057200	Flanking Active TSS	Placenta	Placenta
4	chr15:41055200-41057200	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr15:41055200-41057600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:41055200-41058000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr15:41055400-41056800	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr15:41055400-41056800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr15:41055400-41056800	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr15:41055400-41056800	Flanking Active TSS	HUVEC	blood vessel
11	chr15:41055400-41057000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:41055400-41057000	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr15:41055400-41057000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr15:41055400-41057000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:41055400-41057000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:41055400-41057000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:41055400-41057000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
18	chr15:41055400-41057000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr15:41055400-41057000	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr15:41055400-41057000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
21	chr15:41055400-41057000	Flanking Active TSS	NH-A	brain
22	chr15:41055400-41057200	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr15:41055400-41057200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:41055400-41057200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr15:41055400-41057200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:41055400-41057200	Flanking Active TSS	Colonic Mucosa	Colon
27	chr15:41055400-41057200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr15:41055400-41057200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr15:41055400-41057400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr15:41055400-41057400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr15:41055400-41057400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:41055400-41057400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr15:41055400-41057600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:41055400-41057600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr15:41055400-41057600	Flanking Active TSS	Osteobl	bone
36	chr15:41055400-41058000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr15:41055400-41058000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:41055400-41058000	Flanking Active TSS	NHEK	skin
39	chr15:41055600-41056800	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr15:41055600-41056800	Active TSS	NHDF-Ad	bronchial
41	chr15:41055600-41057000	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr15:41055600-41057000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:41055600-41057000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr15:41055600-41057000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr15:41055600-41057000	Flanking Active TSS	Left Ventricle	heart
46	chr15:41055600-41057000	Active TSS	Ovary	ovary
47	chr15:41055600-41057000	Active TSS	Psoas Muscle	Psoas
48	chr15:41055600-41057000	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr15:41055600-41057200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:41055600-41057200	Active TSS	H9 Cell Line	embryonic stem cell

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