Variant report

Variant	rs61040173
Chromosome Location	chr15:39873887-39873888
allele	A/C
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	EP300	chr15:39873875-39874075	HepG2	liver:	n/a	n/a
2	CTCF	chr15:39873887-39874134	HepG2	liver:	n/a	n/a
3	JUND	chr15:39873861-39874233	H1-hESC	embryonic stem cell:	n/a	n/a
4	HNF4A	chr15:39873873-39874227	HepG2	liver:	n/a	chr15:39873992-39874004 chr15:39873991-39874005 chr15:39873916-39873923
5	TAF1	chr15:39873856-39874202	H1-hESC	embryonic stem cell:	n/a	n/a
6	RFX5	chr15:39873648-39874137	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:39873165-39874278	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
9	RAD21	chr15:39873756-39874335	A549	lung:	n/a	n/a
10	TCF12	chr15:39871518-39874274	A549	lung:	n/a	chr15:39874183-39874190
11	POLR2A	chr15:39872374-39882964	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr15:39872526-39874281	MCF-7	breast:	n/a	n/a
13	POLR2A	chr15:39871542-39884619	MCF10A-Er-Src	breast:	n/a	n/a
14	CTCF	chr15:39873885-39874210	GM12878	blood:	n/a	n/a
15	HNF4A	chr15:39873859-39874185	HepG2	liver:	n/a	chr15:39873992-39874004 chr15:39873991-39874005 chr15:39873916-39873923
16	ATF2	chr15:39873011-39874946	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr15:39872965-39876755	SK-N-SH	brain:	n/a	n/a
18	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
19	POLR2A	chr15:39872827-39889306	SK-N-SH	brain:	n/a	n/a
20	GATA2	chr15:39873871-39874700	HUVEC	blood vessel:	n/a	n/a
21	RAD21	chr15:39873731-39874283	MCF-7	breast:	n/a	n/a
22	GATA3	chr15:39873877-39874220	T-47D	breast:	n/a	n/a
23	NR2F2	chr15:39873413-39874278	MCF-7	breast:	n/a	n/a
24	RAD21	chr15:39873850-39874218	HepG2	liver:	n/a	n/a
25	GTF2F1	chr15:39873801-39874169	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr15:39873785-39874258	HepG2	liver:	n/a	n/a
27	POLR2A	chr15:39872988-39874169	HepG2	liver:	n/a	n/a
28	SMC3	chr15:39873879-39874236	HepG2	liver:	n/a	n/a
29	ELF1	chr15:39873725-39874299	MCF-7	breast:	n/a	n/a
30	JUND	chr15:39873735-39874221	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr15:39873863-39874183	A549	lung:	n/a	n/a
32	CTCF	chr15:39872088-39874388	A549	lung:	n/a	chr15:39872533-39872549 chr15:39873503-39873512 chr15:39872532-39872550 chr15:39874333-39874346 chr15:39873147-39873160
33	MAZ	chr15:39870877-39886058	IMR90	lung:	n/a	chr15:39874192-39874207 chr15:39872697-39872706 chr15:39873005-39873014
34	FOS	chr15:39873108-39874218	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr15:39873815-39874248	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr15:39873870-39874276	A549	lung:	n/a	n/a
37	CHD1	chr15:39871846-39874443	H1-hESC	embryonic stem cell:	n/a	chr15:39872910-39872920
38	FOXA2	chr15:39873767-39874306	A549	lung:	n/a	n/a
39	TAF7	chr15:39873863-39874490	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr15:39871578-39884189	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr15:39873793-39874241	H1-hESC	embryonic stem cell:	n/a	n/a
42	GATA3	chr15:39872904-39874400	A549	lung:	n/a	n/a
43	POLR2A	chr15:39871636-39892218	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr15:39873813-39874201	HepG2	liver:	n/a	n/a
45	POLR2A	chr15:39871327-39893495	HUVEC	blood vessel:	n/a	n/a
46	PML	chr15:39872994-39874330	MCF-7	breast:	n/a	n/a
47	CTCF	chr15:39873877-39874148	SK-N-SH_RA	brain:	n/a	n/a
48	USF2	chr15:39872488-39877080	H1-hESC	embryonic stem cell:	n/a	chr15:39873437-39873453 chr15:39873434-39873450 chr15:39874194-39874207 chr15:39873397-39873413 chr15:39872593-39872609
49	POLR2A	chr15:39873169-39875621	PBDE	blood:	n/a	n/a
50	POLR2A	chr15:39872507-39876756	MCF-7	breast:	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	chr15:39561763..39569547-chr15:39871861..39876512,9	MCF-7	breast:
4	chr15:39457550..39462148-chr15:39871822..39875383,4	MCF-7	breast:
5	chr15:39562139..39567868-chr15:39871478..39875404,11	MCF-7	breast:
6	chr15:38997651..39000510-chr15:39873300..39874931,2	MCF-7	breast:
7	chr15:39872681..39874712-chr15:39877108..39879648,2	K562	blood:
8	chr15:39873532..39876107-chr15:39899045..39902121,3	MCF-7	breast:
9	chr15:39873342..39875967-chr15:39918932..39920569,2	MCF-7	breast:
10	chr15:39873411..39875536-chr15:39928177..39929699,2	MCF-7	breast:
11	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: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10083552	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10520136	0.83[ASN][1000 genomes]
rs12324682	0.83[ASN][1000 genomes]
rs16969307	1.00[EUR][1000 genomes]
rs16969335	0.83[ASN][1000 genomes]
rs16969338	0.83[ASN][1000 genomes]
rs16969352	0.83[ASN][1000 genomes]
rs16969364	1.00[EUR][1000 genomes]
rs16969365	1.00[EUR][1000 genomes]
rs16969384	1.00[EUR][1000 genomes]
rs16969484	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16969573	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16969678	0.83[ASN][1000 genomes]
rs41376748	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41406047	1.00[EUR][1000 genomes]
rs41515347	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4291886	1.00[ASN][1000 genomes]
rs4322636	0.83[ASN][1000 genomes]
rs58677957	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58716252	1.00[EUR][1000 genomes]
rs59146042	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7163020	1.00[EUR][1000 genomes]
rs7172057	1.00[EUR][1000 genomes]
rs74008705	1.00[EUR][1000 genomes]
rs8023525	1.00[EUR][1000 genomes]
rs8029417	1.00[EUR][1000 genomes]
rs8030643	1.00[EUR][1000 genomes]
rs8031289	1.00[EUR][1000 genomes]
rs8033803	1.00[EUR][1000 genomes]
rs8035627	1.00[EUR][1000 genomes]
rs8036035	0.83[ASN][1000 genomes]
rs8043342	1.00[EUR][1000 genomes]
rs878941	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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39871600-39874000	Active TSS	Ovary	ovary
2	chr15:39871600-39874200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:39871600-39875400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:39871600-39875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:39871800-39874000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr15:39871800-39874000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:39871800-39874000	Active TSS	Colon Smooth Muscle	Colon
8	chr15:39871800-39874000	Active TSS	Rectal Smooth Muscle	rectum
9	chr15:39871800-39874000	Active TSS	A549	lung
10	chr15:39871800-39874400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr15:39871800-39874400	Active TSS	Left Ventricle	heart
12	chr15:39871800-39874400	Active TSS	Placenta Amnion	Placenta Amnion
13	chr15:39871800-39874800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:39871800-39874800	Active TSS	Fetal Kidney	kidney
15	chr15:39871800-39875200	Active TSS	Gastric	stomach
16	chr15:39872000-39874000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr15:39872000-39874000	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr15:39872000-39874000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:39872000-39874000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:39872000-39874200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:39872200-39874000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:39872200-39874000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr15:39872200-39874200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr15:39872200-39875200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
25	chr15:39872400-39874000	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr15:39872400-39874000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
27	chr15:39872400-39874000	Active TSS	Fetal Lung	lung
28	chr15:39872400-39874000	Active TSS	Fetal Stomach	stomach
29	chr15:39872400-39874000	Active TSS	NH-A	brain
30	chr15:39872400-39874200	Active TSS	Fetal Intestine Large	intestine
31	chr15:39872400-39874600	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr15:39872400-39874600	Active TSS	HSMMtube	muscle
33	chr15:39872400-39874800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:39872400-39875000	Active TSS	Brain Anterior Caudate	brain
35	chr15:39872400-39876600	Active TSS	Duodenum Mucosa	Duodenum
36	chr15:39872600-39874200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr15:39872600-39874400	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr15:39872600-39874600	Flanking Active TSS	Liver	Liver
39	chr15:39872600-39876800	Active TSS	Small Intestine	intestine
40	chr15:39872600-39882400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:39872800-39874200	Active TSS	Lung	lung
42	chr15:39872800-39874400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
43	chr15:39872800-39874600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
44	chr15:39872800-39875400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr15:39872800-39875400	Active TSS	Psoas Muscle	Psoas
46	chr15:39872800-39875600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
47	chr15:39872800-39877200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:39872800-39881600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:39873000-39874000	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr15:39873000-39874200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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