Variant report

Variant	rs2236741
Chromosome Location	chr15:39874195-39874196
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	JUND	chr15:39873861-39874233	H1-hESC	embryonic stem cell:	n/a	n/a
2	HNF4A	chr15:39873873-39874227	HepG2	liver:	n/a	chr15:39873992-39874004 chr15:39873991-39874005 chr15:39873916-39873923
3	TAF1	chr15:39873856-39874202	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr15:39874080-39874230	HFF-Myc	foreskin:	n/a	n/a
5	POLR2A	chr15:39873165-39874278	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
7	RAD21	chr15:39873756-39874335	A549	lung:	n/a	n/a
8	TCF12	chr15:39871518-39874274	A549	lung:	n/a	chr15:39874183-39874190
9	POLR2A	chr15:39872374-39882964	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr15:39872526-39874281	MCF-7	breast:	n/a	n/a
11	POLR2A	chr15:39871542-39884619	MCF10A-Er-Src	breast:	n/a	n/a
12	CTCF	chr15:39873885-39874210	GM12878	blood:	n/a	n/a
13	NR3C1	chr15:39873896-39874195	A549	lung:	n/a	n/a
14	ATF2	chr15:39873011-39874946	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr15:39872965-39876755	SK-N-SH	brain:	n/a	n/a
16	MXI1	chr15:39874003-39874211	H1-hESC	embryonic stem cell:	n/a	n/a
17	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
18	MYC	chr15:39873914-39874255	MCF-7	breast:	n/a	chr15:39874192-39874207
19	POLR2A	chr15:39872827-39889306	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr15:39874060-39874210	NHDF-neo	bronchial:	n/a	n/a
21	RAD21	chr15:39873916-39874221	A549	lung:	n/a	n/a
22	GATA2	chr15:39873871-39874700	HUVEC	blood vessel:	n/a	n/a
23	MYC	chr15:39873996-39874292	HUVEC	blood vessel:	n/a	chr15:39874192-39874207
24	RAD21	chr15:39873731-39874283	MCF-7	breast:	n/a	n/a
25	GATA3	chr15:39873877-39874220	T-47D	breast:	n/a	n/a
26	NR2F2	chr15:39873413-39874278	MCF-7	breast:	n/a	n/a
27	RAD21	chr15:39873850-39874218	HepG2	liver:	n/a	n/a
28	RAD21	chr15:39873785-39874258	HepG2	liver:	n/a	n/a
29	CTCF	chr15:39873939-39874214	MCF-7	breast:	n/a	n/a
30	SMC3	chr15:39873879-39874236	HepG2	liver:	n/a	n/a
31	ELF1	chr15:39873725-39874299	MCF-7	breast:	n/a	n/a
32	JUND	chr15:39873735-39874221	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr15:39872088-39874388	A549	lung:	n/a	chr15:39872533-39872549 chr15:39873503-39873512 chr15:39872532-39872550 chr15:39874333-39874346 chr15:39873147-39873160
34	MAZ	chr15:39870877-39886058	IMR90	lung:	n/a	chr15:39874192-39874207 chr15:39872697-39872706 chr15:39873005-39873014
35	FOS	chr15:39873108-39874218	HUVEC	blood vessel:	n/a	n/a
36	MAX	chr15:39874006-39874213	NB4	blood:	n/a	chr15:39874192-39874207
37	CTCF	chr15:39873907-39874229	MCF-7	breast:	n/a	n/a
38	NR3C1	chr15:39873920-39874235	A549	lung:	n/a	chr15:39874204-39874213
39	POLR2A	chr15:39873815-39874248	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr15:39873870-39874276	A549	lung:	n/a	n/a
41	CHD1	chr15:39871846-39874443	H1-hESC	embryonic stem cell:	n/a	chr15:39872910-39872920
42	FOXA2	chr15:39873767-39874306	A549	lung:	n/a	n/a
43	RCOR1	chr15:39873943-39874205	HepG2	liver:	n/a	n/a
44	CTCF	chr15:39873918-39874215	MCF-7	breast:	n/a	n/a
45	TAF7	chr15:39873863-39874490	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr15:39871578-39884189	H1-hESC	embryonic stem cell:	n/a	n/a
47	RAD21	chr15:39873793-39874241	H1-hESC	embryonic stem cell:	n/a	n/a
48	GATA3	chr15:39872904-39874400	A549	lung:	n/a	n/a
49	NR3C1	chr15:39873908-39874321	A549	lung:	n/a	chr15:39874204-39874213
50	POLR2A	chr15:39871636-39892218	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:39462462..39474613-chr15:39871091..39879136,29	MCF-7	breast:
2	chr15:39705799..39707909-chr15:39873297..39874835,2	MCF-7	breast:
3	chr15:39694348..39696610-chr15:39874084..39875864,2	MCF-7	breast:
4	chr15:39561763..39569547-chr15:39871861..39876512,9	MCF-7	breast:
5	chr15:39457550..39462148-chr15:39871822..39875383,4	MCF-7	breast:
6	chr15:39562139..39567868-chr15:39871478..39875404,11	MCF-7	breast:
7	chr15:38997651..39000510-chr15:39873300..39874931,2	MCF-7	breast:
8	chr15:39869407..39871427-chr15:39874178..39876262,2	K562	blood:
9	chr15:39872681..39874712-chr15:39877108..39879648,2	K562	blood:
10	chr15:39873532..39876107-chr15:39899045..39902121,3	MCF-7	breast:
11	chr15:39873342..39875967-chr15:39918932..39920569,2	MCF-7	breast:
12	chr15:39873411..39875536-chr15:39928177..39929699,2	MCF-7	breast:
13	chr15:39873405..39876255-chr15:39978051..39980636,2	MCF-7	breast:

Variant related genes	Relation type
THBS1	TF binding region
ENSG00000259345	Chromatin interaction
ENSG00000137801	Chromatin interaction
ENSG00000259423	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2292304	1.00[EUR][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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39871600-39874200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:39871600-39875400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:39871600-39875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:39871800-39874400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:39871800-39874400	Active TSS	Left Ventricle	heart
6	chr15:39871800-39874400	Active TSS	Placenta Amnion	Placenta Amnion
7	chr15:39871800-39874800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:39871800-39874800	Active TSS	Fetal Kidney	kidney
9	chr15:39871800-39875200	Active TSS	Gastric	stomach
10	chr15:39872000-39874200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:39872200-39874200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr15:39872200-39875200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
13	chr15:39872400-39874200	Active TSS	Fetal Intestine Large	intestine
14	chr15:39872400-39874600	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr15:39872400-39874600	Active TSS	HSMMtube	muscle
16	chr15:39872400-39874800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:39872400-39875000	Active TSS	Brain Anterior Caudate	brain
18	chr15:39872400-39876600	Active TSS	Duodenum Mucosa	Duodenum
19	chr15:39872600-39874200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:39872600-39874400	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr15:39872600-39874600	Flanking Active TSS	Liver	Liver
22	chr15:39872600-39876800	Active TSS	Small Intestine	intestine
23	chr15:39872600-39882400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:39872800-39874200	Active TSS	Lung	lung
25	chr15:39872800-39874400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
26	chr15:39872800-39874600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:39872800-39875400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr15:39872800-39875400	Active TSS	Psoas Muscle	Psoas
29	chr15:39872800-39875600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr15:39872800-39877200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:39872800-39881600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:39873000-39874200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
33	chr15:39873000-39874400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
34	chr15:39873200-39874200	Flanking Active TSS	Spleen	Spleen
35	chr15:39873200-39874800	Bivalent/Poised TSS	Thymus	Thymus
36	chr15:39873400-39874200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:39873400-39874200	Active TSS	Fetal Heart	heart
38	chr15:39873400-39874200	Bivalent/Poised TSS	Fetal Thymus	thymus
39	chr15:39873400-39874200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
40	chr15:39873400-39874400	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
41	chr15:39873400-39875000	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr15:39873400-39875000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
43	chr15:39873400-39879200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:39873400-39879400	Weak transcription	Aorta	Aorta
45	chr15:39873400-39879800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
46	chr15:39873400-39880800	Transcr. at gene 5' and 3'	NHLF	lung
47	chr15:39873400-39881600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:39873400-39884200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
49	chr15:39873400-39884200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
50	chr15:39873400-39886800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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