Variant report

Variant	rs2016546
Chromosome Location	chr15:41056440-41056441
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	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	MYC	chr15:41056159-41056467	MCF-7	breast:	n/a	n/a
6	E2F6	chr15:41056052-41056481	A549	lung:	n/a	chr15:41056207-41056216
7	YY1	chr15:41056008-41056477	GM12892	blood:	n/a	chr15:41056192-41056203
8	HEY1	chr15:41055808-41056524	K562	blood:	n/a	n/a
9	POLR2A	chr15:41055920-41056820	GM19193	blood:	n/a	n/a
10	RFX5	chr15:41055334-41056939	Hela-S3	cervix:	n/a	chr15:41055483-41055497
11	POLR2A	chr15:41055349-41059478	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr15:41055852-41056659	HepG2	liver:	n/a	n/a
13	HCFC1	chr15:41055962-41056647	K562	blood:	n/a	n/a
14	ZNF143	chr15:41056114-41056654	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr15:41056360-41056510	Hela-S3	cervix:	n/a	n/a
16	GABPA	chr15:41055993-41056849	K562	blood:	n/a	n/a
17	E2F1	chr15:41055371-41056714	Hela-S3	cervix:	n/a	chr15:41056207-41056216 chr15:41055940-41055949 chr15:41055502-41055511 chr15:41056701-41056713
18	CTCF	chr15:41056040-41056647	H1-hESC	embryonic stem cell:	n/a	chr15:41056060-41056073 chr15:41056345-41056354
19	CTCF	chr15:41055918-41056531	A549	lung:	n/a	chr15:41056060-41056073 chr15:41056345-41056354
20	PML	chr15:41056143-41056681	MCF-7	breast:	n/a	n/a
21	CTCF	chr15:41056063-41056494	K562	blood:	n/a	chr15:41056345-41056354
22	UBTF	chr15:41055478-41056937	K562	blood:	n/a	n/a
23	MAX	chr15:41056079-41056655	NB4	blood:	n/a	n/a
24	YY1	chr15:41056094-41056581	ECC-1	luminal epithelium:	n/a	chr15:41056192-41056203
25	POLR2A	chr15:41055417-41056733	HepG2	liver:	n/a	n/a
26	ZBTB7A	chr15:41055540-41056828	ECC-1	luminal epithelium:	n/a	n/a
27	NFYB	chr15:41055883-41056626	Hela-S3	cervix:	n/a	chr15:41056203-41056218 chr15:41056203-41056218 chr15:41056206-41056216 chr15:41056205-41056220
28	POLR2A	chr15:41055937-41056687	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr15:41056163-41056502	A549	lung:	n/a	n/a
30	TAF1	chr15:41055959-41056458	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr15:41056044-41056821	GM12878	blood:	n/a	n/a
32	MAX	chr15:41055194-41056853	HepG2	liver:	n/a	chr15:41056062-41056072 chr15:41055747-41055757
33	TFAP2A	chr15:41055325-41057035	Hela-S3	cervix:	n/a	chr15:41056124-41056132 chr15:41056124-41056132 chr15:41055719-41055731 chr15:41056124-41056132
34	CTCF	chr15:41056021-41056452	K562	blood:	n/a	chr15:41056060-41056073 chr15:41056345-41056354
35	CHD2	chr15:41056089-41056683	H1-hESC	embryonic stem cell:	n/a	n/a
36	E2F4	chr15:41055331-41056747	K562	blood:	n/a	chr15:41056207-41056216 chr15:41055940-41055949 chr15:41055502-41055511 chr15:41055526-41055537 chr15:41056701-41056713
37	POLR2A	chr15:41055827-41056644	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr15:41055791-41056714	HepG2	liver:	n/a	n/a
39	CTCF	chr15:41056078-41056457	GM12878	blood:	n/a	chr15:41056345-41056354
40	NFYA	chr15:41055891-41056759	Hela-S3	cervix:	n/a	chr15:41056203-41056218 chr15:41056199-41056217 chr15:41056203-41056218 chr15:41056206-41056216
41	CBX3	chr15:41055232-41056593	K562	blood:	n/a	n/a
42	CHD2	chr15:41055906-41056527	HepG2	liver:	n/a	n/a
43	POLR2A	chr15:41055876-41056515	GM12892	blood:	n/a	n/a
44	CREB1	chr15:41055314-41056830	HepG2	liver:	n/a	n/a
45	SIN3AK20	chr15:41055293-41056904	MCF-7	breast:	n/a	n/a
46	ELF1	chr15:41055434-41056906	MCF-7	breast:	n/a	chr15:41056583-41056592 chr15:41056679-41056688 chr15:41056678-41056687
47	MAX	chr15:41055326-41056608	H1-hESC	embryonic stem cell:	n/a	chr15:41056062-41056072 chr15:41055747-41055757
48	TAF1	chr15:41055785-41056791	HepG2	liver:	n/a	n/a
49	NFIC	chr15:41056286-41056798	GM12878	blood:	n/a	n/a
50	POLR2A	chr15:41056173-41056732	GM12891	blood:	n/a	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	chr15:41042059..41049706-chr15:41053861..41061949,15	MCF-7	breast:
4	chr15:40985800..40990095-chr15:41055400..41057901,4	K562	blood:
5	chr15:41055895..41056540-chr7:66767078..66768033,2	Hela-S3	cervix:
6	chr15:41056057..41057921-chr15:41407305..41409021,2	K562	blood:
7	chr12:120729277..120729973-chr15:41055717..41056485,2	Hela-S3	cervix:
8	chr15:41054213..41057951-chr15:41097645..41100150,5	K562	blood:
9	chr15:41056175..41056885-chr3:196159214..196159919,2	Hela-S3	cervix:
10	chr15:41056057..41058777-chr15:41406413..41409021,2	K562	blood:
11	chr15:41055458..41058081-chr15:41065711..41068133,2	K562	blood:
12	chr15:41054628..41058503-chr15:41058814..41065530,15	K562	blood:
13	chr15:41036948..41038953-chr15:41054723..41057087,2	K562	blood:
14	chr15:41055716..41060288-chr15:41072655..41077591,4	MCF-7	breast:
15	chr15:41056183..41056694-chr20:49347609..49348507,2	Hela-S3	cervix:

Variant related genes	Relation type
GCHFR	TF binding region
ENSG00000166140	Chromatin interaction
ENSG00000067601	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000163960	Chromatin interaction
ENSG00000188277	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000106610	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12915171	1.00[JPT][hapmap]
rs16971001	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs2301176	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2898999	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3784290	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs57096780	1.00[ASN][1000 genomes]
rs57272245	1.00[ASN][1000 genomes]
rs7174651	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7175221	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7179899	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73398513	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398545	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8025558	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029321	1.00[ASN][1000 genomes]
rs8031526	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][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	chr15:41055200-41056800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:41055200-41057200	Flanking Active TSS	Placenta	Placenta
5	chr15:41055200-41057200	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr15:41055200-41057600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:41055200-41058000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr15:41055400-41056600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:41055400-41056600	Flanking Active TSS	Pancreas	Pancrea
10	chr15:41055400-41056600	Flanking Active TSS	Right Ventricle	heart
11	chr15:41055400-41056800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr15:41055400-41056800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr15:41055400-41056800	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr15:41055400-41056800	Flanking Active TSS	HUVEC	blood vessel
15	chr15:41055400-41057000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:41055400-41057000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr15:41055400-41057000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr15:41055400-41057000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:41055400-41057000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:41055400-41057000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:41055400-41057000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
22	chr15:41055400-41057000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr15:41055400-41057000	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr15:41055400-41057000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
25	chr15:41055400-41057000	Flanking Active TSS	NH-A	brain
26	chr15:41055400-41057200	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr15:41055400-41057200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:41055400-41057200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr15:41055400-41057200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:41055400-41057200	Flanking Active TSS	Colonic Mucosa	Colon
31	chr15:41055400-41057200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr15:41055400-41057200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr15:41055400-41057400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr15:41055400-41057400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr15:41055400-41057400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:41055400-41057400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr15:41055400-41057600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:41055400-41057600	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr15:41055400-41057600	Flanking Active TSS	Osteobl	bone
40	chr15:41055400-41058000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr15:41055400-41058000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:41055400-41058000	Flanking Active TSS	NHEK	skin
43	chr15:41055600-41056600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:41055600-41056600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
45	chr15:41055600-41056600	Flanking Active TSS	HMEC	breast
46	chr15:41055600-41056800	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr15:41055600-41056800	Active TSS	NHDF-Ad	bronchial
48	chr15:41055600-41057000	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr15:41055600-41057000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:41055600-41057000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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