Variant report

Variant	rs604057
Chromosome Location	chr15:59157289-59157290
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	TBP	chr15:59156693-59157370	HepG2	liver:	n/a	chr15:59157139-59157150
2	POLR2A	chr15:59156751-59157497	HepG2	liver:	n/a	n/a
3	RAD21	chr15:59156863-59157644	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:59156745-59158918	NB4	blood:	n/a	n/a
5	POLR2A	chr15:59156453-59158833	HepG2	liver:	n/a	n/a
6	TAF1	chr15:59156788-59157594	HepG2	liver:	n/a	n/a
7	HEY1	chr15:59156647-59157389	HepG2	liver:	n/a	chr15:59157174-59157189
8	ELF1	chr15:59156975-59157530	GM12878	blood:	n/a	chr15:59157268-59157277 chr15:59157068-59157080
9	TAF1	chr15:59157232-59157511	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYBL2	chr15:59156616-59157308	HepG2	liver:	n/a	n/a
11	CHD2	chr15:59156789-59158056	HepG2	liver:	n/a	n/a
12	RAD21	chr15:59156823-59157591	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr15:59156791-59157528	HepG2	liver:	n/a	n/a
14	RFX5	chr15:59156870-59157333	HepG2	liver:	n/a	n/a
15	E2F6	chr15:59156797-59157785	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr15:59156906-59157556	H1-hESC	embryonic stem cell:	n/a	n/a
17	BHLHE40	chr15:59156764-59157975	HepG2	liver:	n/a	n/a
18	HNF4G	chr15:59156652-59157389	HepG2	liver:	n/a	chr15:59156973-59156988
19	ZEB1	chr15:59157188-59157434	GM12878	blood:	n/a	n/a
20	MAX	chr15:59156384-59158233	HepG2	liver:	n/a	chr15:59157169-59157178
21	MXI1	chr15:59156672-59158015	HepG2	liver:	n/a	n/a
22	MAX	chr15:59156808-59157864	H1-hESC	embryonic stem cell:	n/a	chr15:59157169-59157178
23	HMGN3	chr15:59157019-59157393	K562	blood:	n/a	n/a
24	MAX	chr15:59156674-59157911	HepG2	liver:	n/a	chr15:59157169-59157178
25	MXI1	chr15:59157250-59157383	H1-hESC	embryonic stem cell:	n/a	n/a
26	EP300	chr15:59156791-59157370	HepG2	liver:	n/a	n/a
27	POLR2A	chr15:59156646-59158082	HepG2	liver:	n/a	n/a
28	EP300	chr15:59156663-59157306	HepG2	liver:	n/a	n/a
29	SP1	chr15:59156642-59157293	HepG2	liver:	n/a	n/a
30	MAX	chr15:59156508-59158172	NB4	blood:	n/a	chr15:59157169-59157178
31	E2F6	chr15:59156775-59157837	H1-hESC	embryonic stem cell:	n/a	n/a
32	HDAC2	chr15:59156691-59157302	HepG2	liver:	n/a	n/a
33	GTF2F1	chr15:59157143-59157476	H1-hESC	embryonic stem cell:	n/a	n/a
34	FOXA1	chr15:59156714-59157306	HepG2	liver:	n/a	n/a
35	REST	chr15:59156828-59157325	HepG2	liver:	n/a	chr15:59157010-59157023 chr15:59157210-59157223
36	ARID3A	chr15:59156691-59157389	HepG2	liver:	n/a	n/a
37	HNF4A	chr15:59156777-59157362	HepG2	liver:	n/a	n/a
38	SIN3A	chr15:59156802-59157448	H1-hESC	embryonic stem cell:	n/a	chr15:59157381-59157390 chr15:59157179-59157188 chr15:59157243-59157252 chr15:59157390-59157399
39	POLR2A	chr15:59156720-59158117	HepG2	liver:	n/a	n/a
40	YY1	chr15:59156788-59157679	HepG2	liver:	n/a	chr15:59157176-59157190 chr15:59157524-59157535
41	MAX	chr15:59156810-59157485	H1-hESC	embryonic stem cell:	n/a	chr15:59157169-59157178
42	TBP	chr15:59156820-59157434	H1-hESC	embryonic stem cell:	n/a	chr15:59157139-59157150
43	POLR2A	chr15:59156716-59158766	HepG2	liver:	n/a	n/a
44	ZNF143	chr15:59157274-59157354	H1-hESC	embryonic stem cell:	n/a	n/a
45	MYC	chr15:59156638-59158881	NB4	blood:	n/a	chr15:59157169-59157178
46	MYBL2	chr15:59156663-59157751	HepG2	liver:	n/a	n/a
47	SIN3AK20	chr15:59156766-59157328	HepG2	liver:	n/a	n/a
48	POLR2A	chr15:59156828-59157885	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr15:59156718-59157635	H1-hESC	embryonic stem cell:	n/a	n/a
50	CEBPB	chr15:59157246-59157444	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000259353	TF binding region
RNF111	TF binding region
ENSG00000242747	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10518991	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10518992	0.95[EUR][1000 genomes]
rs1078001	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1092172	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11071401	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11630160	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11636723	0.95[EUR][1000 genomes]
rs11637077	0.95[EUR][1000 genomes]
rs11858989	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12438961	0.83[EUR][1000 genomes]
rs12440904	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12443436	0.88[EUR][1000 genomes]
rs12595482	0.92[EUR][1000 genomes]
rs12914723	0.92[EUR][1000 genomes]
rs17302038	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17302045	0.95[EUR][1000 genomes]
rs173214	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2013117	0.86[EUR][1000 genomes]
rs2279719	0.89[EUR][1000 genomes]
rs28473013	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28529423	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28538484	0.95[EUR][1000 genomes]
rs28641638	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28709922	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35477914	0.95[EUR][1000 genomes]
rs431414	0.95[EUR][1000 genomes]
rs592407	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs637918	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs677933	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs694918	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7173317	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8035628	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs813219	0.95[EUR][1000 genomes]
rs813220	0.80[AFR][1000 genomes];0.88[EUR][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	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1035640	chr15:59105360-59190930	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv904270	chr15:59140329-59238415	Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59067000-59157800	Weak transcription	Hela-S3	cervix
2	chr15:59111800-59159600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:59120000-59169000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:59145000-59166600	Weak transcription	HSMMtube	muscle
5	chr15:59147200-59169000	Weak transcription	K562	blood
6	chr15:59147600-59174600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:59147800-59157400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:59148000-59168600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:59148000-59169000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:59151200-59165400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:59154600-59170200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr15:59156400-59157600	Enhancers	Fetal Kidney	kidney
13	chr15:59156600-59157400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:59156600-59157800	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr15:59156600-59158000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr15:59156600-59158200	Active TSS	Duodenum Mucosa	Duodenum
17	chr15:59156600-59158200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr15:59156800-59157400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:59156800-59157400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:59156800-59157400	Active TSS	Brain Angular Gyrus	brain
21	chr15:59156800-59157400	Enhancers	Fetal Lung	lung
22	chr15:59156800-59157400	Enhancers	Placenta	Placenta
23	chr15:59156800-59157400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr15:59156800-59157600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr15:59156800-59157600	Active TSS	Primary hematopoietic stem cells	blood
26	chr15:59156800-59157600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr15:59156800-59157800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
28	chr15:59156800-59157800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr15:59156800-59157800	Enhancers	Spleen	Spleen
30	chr15:59156800-59158000	Active TSS	Colon Smooth Muscle	Colon
31	chr15:59156800-59158000	Enhancers	Lung	lung
32	chr15:59156800-59158000	Flanking Active TSS	Pancreas	Pancrea
33	chr15:59156800-59158400	Active TSS	Fetal Intestine Large	intestine
34	chr15:59156800-59158600	Active TSS	HepG2	liver
35	chr15:59157000-59157400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:59157000-59157400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:59157000-59157400	Flanking Active TSS	Colonic Mucosa	Colon
38	chr15:59157000-59157400	Enhancers	Esophagus	oesophagus
39	chr15:59157000-59157400	Flanking Active TSS	Left Ventricle	heart
40	chr15:59157000-59157400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
41	chr15:59157000-59157400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr15:59157000-59157400	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr15:59157000-59157600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr15:59157000-59157600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:59157000-59157600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
46	chr15:59157000-59157600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:59157000-59157600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr15:59157000-59157600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:59157000-59157600	Active TSS	Brain Germinal Matrix	brain
50	chr15:59157000-59157600	Bivalent Enhancer	Fetal Brain Male	brain

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