Variant report

Variant	rs592407
Chromosome Location	chr15:59157540-59157541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr15:59156863-59157644	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:59156745-59158918	NB4	blood:	n/a	n/a
3	POLR2A	chr15:59156453-59158833	HepG2	liver:	n/a	n/a
4	TAF1	chr15:59156788-59157594	HepG2	liver:	n/a	n/a
5	CHD2	chr15:59156789-59158056	HepG2	liver:	n/a	n/a
6	RAD21	chr15:59156823-59157591	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr15:59156797-59157785	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:59156906-59157556	H1-hESC	embryonic stem cell:	n/a	n/a
9	BHLHE40	chr15:59156764-59157975	HepG2	liver:	n/a	n/a
10	MAX	chr15:59156384-59158233	HepG2	liver:	n/a	chr15:59157169-59157178
11	MXI1	chr15:59156672-59158015	HepG2	liver:	n/a	n/a
12	MAX	chr15:59156808-59157864	H1-hESC	embryonic stem cell:	n/a	chr15:59157169-59157178
13	MAX	chr15:59156674-59157911	HepG2	liver:	n/a	chr15:59157169-59157178
14	POLR2A	chr15:59157509-59158098	HepG2	liver:	n/a	n/a
15	POLR2A	chr15:59156646-59158082	HepG2	liver:	n/a	n/a
16	MAX	chr15:59156508-59158172	NB4	blood:	n/a	chr15:59157169-59157178
17	E2F6	chr15:59156775-59157837	H1-hESC	embryonic stem cell:	n/a	n/a
18	HEY1	chr15:59157531-59158131	HepG2	liver:	n/a	n/a
19	POLR2A	chr15:59156720-59158117	HepG2	liver:	n/a	n/a
20	YY1	chr15:59156788-59157679	HepG2	liver:	n/a	chr15:59157176-59157190 chr15:59157524-59157535
21	POLR2A	chr15:59156716-59158766	HepG2	liver:	n/a	n/a
22	MYC	chr15:59156638-59158881	NB4	blood:	n/a	chr15:59157169-59157178
23	MYBL2	chr15:59156663-59157751	HepG2	liver:	n/a	n/a
24	POLR2A	chr15:59156828-59157885	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr15:59156718-59157635	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr15:59156643-59158751	HepG2	liver:	n/a	n/a
27	TAF1	chr15:59156790-59157645	HepG2	liver:	n/a	n/a
28	CHD2	chr15:59157172-59157651	H1-hESC	embryonic stem cell:	n/a	n/a
29	HEY1	chr15:59156646-59158153	HepG2	liver:	n/a	chr15:59157174-59157189
30	MAX	chr15:59156592-59158157	HepG2	liver:	n/a	chr15:59157169-59157178
31	POLR2A	chr15:59156652-59158138	HepG2	liver:	n/a	n/a
32	MAX	chr15:59156706-59157802	H1-hESC	embryonic stem cell:	n/a	chr15:59157169-59157178

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:59157523-59157573	AG04450	lung:	fetal
2	chr15:59157523-59157573	HRPEpiC	eye:	n/a
3	chr15:59157523-59157573	ECC-1	luminal epithelium:	n/a
4	chr15:59157523-59157573	SK-N-SH_RA	brain:	n/a
5	chr15:59157523-59157573	Caco-2	colon:	n/a
6	chr15:59157523-59157573	T-47D	breast:	n/a
7	chr15:59157523-59157573	MCF10A-Er-Src	breast:	n/a
8	chr15:59157523-59157573	BE2_C	brain:	n/a
9	chr15:59157523-59157573	GM06990	blood:	n/a
10	chr15:59157523-59157573	AG09309	skin:	n/a
11	chr15:59157523-59157573	BJ	skin:	n/a
12	chr15:59157523-59157573	HIPEpiC	eye:	n/a
13	chr15:59157523-59157573	HL-60	blood:	n/a
14	chr15:59157523-59157573	Hepatocyte	liver:	n/a
15	chr15:59157523-59157573	LNCaP	prostate:	n/a
16	chr15:59157523-59157573	HRE	kidney:	n/a
17	chr15:59157523-59157573	HRCEpiC	kidney:	n/a
18	chr15:59157523-59157573	U87	brain:	n/a
19	chr15:59157523-59157573	RPTEC	kidney:	n/a
20	chr15:59157523-59157573	HNPCEpiC	eye:	n/a
21	chr15:59157523-59157573	GM19239	blood:	n/a
22	chr15:59157523-59157573	NB4	blood:	n/a
23	chr15:59157523-59157573	GM12892	blood:	n/a
24	chr15:59157523-59157573	PrEC	prostate:	n/a
25	chr15:59157523-59157573	A549	lung:	n/a
26	chr15:59157523-59157573	HMEC	breast:	n/a
27	chr15:59157523-59157573	HCF	heart:	n/a
28	chr15:59157523-59157573	AG04449	skin:	fetal
29	chr15:59157523-59157573	HCT-116	colon:	n/a
30	chr15:59157523-59157573	ProgFib	skin:	n/a
31	chr15:59157523-59157573	Jurkat	blood:	n/a
32	chr15:59157523-59157573	HepG2	liver:	n/a
33	chr15:59157523-59157573	GM12878	blood:	n/a
34	chr15:59157523-59157573	HPAEpiC	pulmonary alveolar:	n/a
35	chr15:59157523-59157573	SAEC	small airway:	n/a
36	chr15:59157523-59157573	H1-hESC	embryonic stem cell:	embryo
37	chr15:59157523-59157573	NHBE	bronchial:	n/a
38	chr15:59157523-59157573	HAEpiC	amniotic membrane:	n/a
39	chr15:59157523-59157573	MCF-7	breast:	n/a
40	chr15:59157523-59157573	HEK293	kidney:	embryo
41	chr15:59157523-59157573	HCM	heart:	n/a
42	chr15:59157523-59157573	HCPEpiC	choroid plexus:	n/a
43	chr15:59157523-59157573	HUVEC	blood vessel:	n/a
44	chr15:59157523-59157573	HEEpiC	esophagus:	n/a
45	chr15:59157523-59157573	AG09319	gingival:	n/a
46	chr15:59157523-59157573	GM12891	blood:	n/a
47	chr15:59157523-59157573	CMK	blood:	n/a
48	chr15:59157523-59157573	SKMC	muscle:	n/a
49	chr15:59157523-59157573	IMR90	lung:	fetal
50	chr15:59157523-59157573	ovcar-3	ovarian:	n/a

No data

Variant related genes	Relation type
ENSG00000242747	TF binding region
ENSG00000259353	TF binding region
ENSG00000242747	CpG island
ENSG00000259353	CpG island

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10518991	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10518992	0.94[EUR][1000 genomes]
rs1078001	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1092172	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11071401	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11630160	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11636723	0.94[EUR][1000 genomes]
rs11637077	0.94[EUR][1000 genomes]
rs11858989	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12438918	0.82[EUR][1000 genomes]
rs12438961	0.86[EUR][1000 genomes]
rs12440904	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12443436	0.86[EUR][1000 genomes]
rs12595482	0.91[EUR][1000 genomes]
rs12914723	0.91[EUR][1000 genomes]
rs17302038	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17302045	0.94[EUR][1000 genomes]
rs173214	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2013117	0.85[EUR][1000 genomes]
rs2279719	0.87[EUR][1000 genomes]
rs28473013	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28529423	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28538484	0.94[EUR][1000 genomes]
rs28641638	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28709922	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35477914	0.94[EUR][1000 genomes]
rs431414	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs604057	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs637918	0.89[EUR][1000 genomes]
rs677933	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs694918	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7173317	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8035628	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs813219	0.92[EUR][1000 genomes]
rs813220	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv977720	chr15:59157444-59165373	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 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	chr15:59148000-59168600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:59148000-59169000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:59151200-59165400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:59154600-59170200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:59156400-59157600	Enhancers	Fetal Kidney	kidney
12	chr15:59156600-59157800	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr15:59156600-59158000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr15:59156600-59158200	Active TSS	Duodenum Mucosa	Duodenum
15	chr15:59156600-59158200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr15:59156800-59157600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:59156800-59157600	Active TSS	Primary hematopoietic stem cells	blood
18	chr15:59156800-59157600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr15:59156800-59157800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
20	chr15:59156800-59157800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr15:59156800-59157800	Enhancers	Spleen	Spleen
22	chr15:59156800-59158000	Active TSS	Colon Smooth Muscle	Colon
23	chr15:59156800-59158000	Enhancers	Lung	lung
24	chr15:59156800-59158000	Flanking Active TSS	Pancreas	Pancrea
25	chr15:59156800-59158400	Active TSS	Fetal Intestine Large	intestine
26	chr15:59156800-59158600	Active TSS	HepG2	liver
27	chr15:59157000-59157600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:59157000-59157600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:59157000-59157600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr15:59157000-59157600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr15:59157000-59157600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr15:59157000-59157600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:59157000-59157600	Active TSS	Brain Germinal Matrix	brain
34	chr15:59157000-59157600	Bivalent Enhancer	Fetal Brain Male	brain
35	chr15:59157000-59157600	Active TSS	Fetal Brain Female	brain
36	chr15:59157000-59157600	Flanking Active TSS	Psoas Muscle	Psoas
37	chr15:59157000-59157600	Flanking Active TSS	Right Atrium	heart
38	chr15:59157000-59157600	Active TSS	Stomach Mucosa	stomach
39	chr15:59157000-59157600	Enhancers	NH-A	brain
40	chr15:59157000-59157600	Enhancers	NHDF-Ad	bronchial
41	chr15:59157000-59157800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr15:59157000-59157800	Active TSS	Primary B cells from cord blood	blood
43	chr15:59157000-59157800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:59157000-59157800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:59157000-59157800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:59157000-59157800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr15:59157000-59157800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:59157000-59157800	Active TSS	Brain Substantia Nigra	brain
49	chr15:59157000-59157800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr15:59157000-59158000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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