Variant report

Variant	rs3825942
Chromosome Location	chr15:74219582-74219583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr15:74219548-74221127	MCF-7	breast:	n/a	n/a
2	RCOR1	chr15:74218148-74219871	IMR90	lung:	n/a	n/a
3	ZBTB7A	chr15:74219366-74220638	ECC-1	luminal epithelium:	n/a	chr15:74220350-74220359 chr15:74220286-74220294
4	MAX	chr15:74218463-74220913	MCF-7	breast:	n/a	n/a
5	EP300	chr15:74219543-74220424	ECC-1	luminal epithelium:	n/a	n/a
6	ZBTB7A	chr15:74219034-74220559	ECC-1	luminal epithelium:	n/a	chr15:74220350-74220359 chr15:74220286-74220294
7	POLR2A	chr15:74219345-74219787	HCT-116	colon:	n/a	n/a
8	MAZ	chr15:74216078-74220816	IMR90	lung:	n/a	n/a
9	NFIC	chr15:74218412-74220406	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr15:74218425-74220724	ProgFib	skin:	n/a	n/a
11	MXI1	chr15:74217976-74222304	IMR90	lung:	n/a	n/a
12	POLR2A	chr15:74218504-74220498	IMR90	lung:	n/a	n/a
13	POLR2A	chr15:74218128-74220905	MCF-7	breast:	n/a	n/a
14	POLR2A	chr15:74218562-74220432	MCF-7	breast:	n/a	n/a
15	POLR2A	chr15:74219504-74220316	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr15:74219368-74220472	MCF-7	breast:	n/a	n/a
17	MAX	chr15:74218460-74220440	ECC-1	luminal epithelium:	n/a	n/a
18	TAF1	chr15:74218531-74219754	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr15:74218518-74220264	ECC-1	luminal epithelium:	n/a	n/a
20	EP300	chr15:74218396-74220477	ECC-1	luminal epithelium:	n/a	chr15:74218605-74218618
21	POLR2A	chr15:74218273-74219818	U87	brain:	n/a	n/a
22	POLR2A	chr15:74218435-74220511	MCF-7	breast:	n/a	n/a
23	TCF12	chr15:74218425-74220518	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr15:74218587-74219799	ECC-1	luminal epithelium:	n/a	n/a
25	NFIC	chr15:74218376-74219781	ECC-1	luminal epithelium:	n/a	n/a
26	HDAC2	chr15:74219413-74220583	MCF-7	breast:	n/a	n/a
27	TCF12	chr15:74218309-74219834	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr15:74219281-74220553	HCT-116	colon:	n/a	n/a
29	SIN3A	chr15:74218455-74220335	H1-hESC	embryonic stem cell:	n/a	n/a
30	SIN3AK20	chr15:74219009-74220314	PANC-1	pancreas:	n/a	n/a
31	NR2F2	chr15:74218457-74220947	MCF-7	breast:	n/a	n/a
32	POLR2A	chr15:74219572-74220355	HCT-116	colon:	n/a	n/a
33	GABPA	chr15:74219378-74219679	K562	blood:	n/a	n/a
34	POLR2A	chr15:74219520-74220314	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr15:74217872-74240199	U87	brain:	n/a	n/a
36	MAX	chr15:74219409-74220440	MCF-7	breast:	n/a	n/a
37	CHD1	chr15:74217903-74221545	IMR90	lung:	n/a	n/a
38	POLR2A	chr15:74215819-74242527	U87	brain:	n/a	n/a
39	MAX	chr15:74218529-74219812	H1-hESC	embryonic stem cell:	n/a	n/a
40	EGR1	chr15:74219576-74219862	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:74217306..74220336-chr15:74236509..74239961,4	MCF-7	breast:
2	chr15:72523731..72525453-chr15:74219224..74220936,2	MCF-7	breast:
3	chr15:74163735..74170089-chr15:74218002..74222715,6	MCF-7	breast:

No data

Variant related genes	Relation type
LOXL1-AS1	TF binding region
ENSG00000067225	Chromatin interaction
ENSG00000260624	Chromatin interaction
ENSG00000167139	Chromatin interaction
ENSG00000129038	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1078967	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1550437	1.00[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs28522673	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74026308	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034017	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041642	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041685	1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8042039	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043335	chr15:74078689-74241186	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1603	chr15:74191222-74235733	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv3324978	chr15:74218524-74221272	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Glaucoma (exfoliation)	17690259	GWAS catalog

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74216800-74220800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr15:74217200-74219600	Weak transcription	A549	lung
3	chr15:74217800-74220400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:74218000-74220000	Weak transcription	Hela-S3	cervix
5	chr15:74218200-74221200	Active TSS	Aorta	Aorta
6	chr15:74218400-74219600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr15:74218400-74219600	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr15:74218400-74219800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:74218400-74219800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:74218400-74219800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:74218400-74219800	Flanking Active TSS	Fetal Muscle Leg	muscle
12	chr15:74218400-74219800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr15:74218400-74220400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr15:74218400-74220600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:74218400-74220800	Flanking Active TSS	HMEC	breast
16	chr15:74218400-74221000	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr15:74218400-74221200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr15:74218400-74221200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr15:74218600-74220200	Active TSS	Colon Smooth Muscle	Colon
20	chr15:74218600-74220400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:74218600-74220400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:74218600-74220400	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr15:74218600-74220400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr15:74218600-74220400	Weak transcription	Fetal Heart	heart
25	chr15:74218600-74220600	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr15:74218600-74220600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:74218600-74220600	Active TSS	NHLF	lung
28	chr15:74218600-74220600	Active TSS	Osteobl	bone
29	chr15:74218600-74220800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:74218600-74221000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr15:74218600-74221200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:74218600-74221200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:74218600-74221200	Active TSS	HSMM	muscle
34	chr15:74218600-74221200	Active TSS	NH-A	brain
35	chr15:74218600-74221200	Active TSS	NHDF-Ad	bronchial
36	chr15:74218600-74221400	Active TSS	HSMMtube	muscle
37	chr15:74218800-74219600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:74218800-74219600	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr15:74218800-74219600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
40	chr15:74218800-74219600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr15:74218800-74219800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:74218800-74219800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr15:74218800-74219800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
44	chr15:74218800-74219800	Flanking Active TSS	Right Ventricle	heart
45	chr15:74218800-74219800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
46	chr15:74218800-74219800	Flanking Active TSS	HUVEC	blood vessel
47	chr15:74218800-74220000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
48	chr15:74218800-74220000	Active TSS	Brain Angular Gyrus	brain
49	chr15:74218800-74220400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr15:74218800-74220400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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