Variant report

Variant	rs72627094
Chromosome Location	chr3:23987261-23987262
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	POLR2A	chr3:23987142-23987892	K562	blood:	n/a	n/a
2	HEY1	chr3:23987159-23987423	K562	blood:	n/a	chr3:23987373-23987388 chr3:23987375-23987390
3	CEBPB	chr3:23987205-23987796	MCF-7	breast:	n/a	n/a
4	TBL1XR1	chr3:23987260-23988383	K562	blood:	n/a	n/a
5	MAX	chr3:23986061-23988244	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
6	POLR2A	chr3:23986710-23988459	H1-hESC	embryonic stem cell:	n/a	n/a
7	YY1	chr3:23987108-23987764	H1-hESC	embryonic stem cell:	n/a	chr3:23987439-23987448 chr3:23987442-23987451 chr3:23987439-23987453 chr3:23987436-23987450 chr3:23987437-23987451 chr3:23987443-23987454 chr3:23987153-23987162 chr3:23987437-23987448 chr3:23987436-23987445
8	MAX	chr3:23986260-23988309	HCT-116	colon:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
9	YY1	chr3:23987182-23987954	GM12891	blood:	n/a	chr3:23987439-23987448 chr3:23987442-23987451 chr3:23987439-23987453 chr3:23987436-23987450 chr3:23987437-23987451 chr3:23987443-23987454 chr3:23987437-23987448 chr3:23987436-23987445
10	IRF1	chr3:23987225-23988263	K562	blood:	n/a	chr3:23987564-23987578
11	EP300	chr3:23987162-23987486	H1-hESC	embryonic stem cell:	n/a	chr3:23987437-23987453 chr3:23987380-23987389 chr3:23987373-23987389 chr3:23987374-23987390 chr3:23987438-23987447
12	SIN3AK20	chr3:23987183-23988106	A549	lung:	n/a	n/a
13	HDAC2	chr3:23987260-23988019	H1-hESC	embryonic stem cell:	n/a	chr3:23987377-23987386
14	FOXA2	chr3:23987163-23987771	A549	lung:	n/a	n/a
15	FOXA1	chr3:23987182-23987548	T-47D	breast:	n/a	n/a
16	POLR2A	chr3:23986575-23988289	MCF10A-Er-Src	breast:	n/a	n/a
17	MYC	chr3:23987208-23987889	HepG2	liver:	n/a	chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
18	POLR2A	chr3:23986444-23988585	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr3:23986467-23988139	Raji	blood:	n/a	n/a
20	PML	chr3:23987217-23988290	GM12878	blood:	n/a	chr3:23988133-23988142
21	FOXP2	chr3:23987193-23987940	PFSK-1	brain:	n/a	n/a
22	CREB1	chr3:23987157-23988267	GM12878	blood:	n/a	chr3:23987593-23987606
23	ATF3	chr3:23987204-23987798	A549	lung:	n/a	chr3:23987584-23987604 chr3:23987374-23987383
24	TFAP2C	chr3:23987172-23988268	Hela-S3	cervix:	n/a	chr3:23987581-23987596
25	CEBPB	chr3:23987219-23987865	HepG2	liver:	n/a	n/a
26	CEBPB	chr3:23987258-23988137	A549	lung:	n/a	n/a
27	MAX	chr3:23987170-23988287	Hela-S3	cervix:	n/a	chr3:23988135-23988144 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
28	FOXA1	chr3:23987198-23987733	T-47D	breast:	n/a	n/a
29	TEAD4	chr3:23987169-23988113	ECC-1	luminal epithelium:	n/a	n/a
30	BHLHE40	chr3:23987153-23988334	HepG2	liver:	n/a	chr3:23987153-23987169 chr3:23987430-23987446 chr3:23987438-23987454 chr3:23987441-23987457 chr3:23987189-23987205
31	TAF7	chr3:23986576-23988026	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:23986438-23987906	HEK293	kidney:	n/a	n/a
33	BHLHE40	chr3:23987235-23987558	HepG2	liver:	n/a	chr3:23987430-23987446 chr3:23987438-23987454 chr3:23987441-23987457
34	TCF7L2	chr3:23986399-23987994	HCT-116	colon:	n/a	n/a
35	BCL3	chr3:23987177-23988255	A549	lung:	n/a	chr3:23987548-23987561 chr3:23987438-23987451 chr3:23987888-23987897 chr3:23987436-23987449 chr3:23987440-23987449 chr3:23987439-23987452 chr3:23987442-23987455 chr3:23987567-23987576 chr3:23987437-23987446
36	POLR2A	chr3:23986629-23988032	NB4	blood:	n/a	n/a
37	EP300	chr3:23987167-23988099	HepG2	liver:	n/a	chr3:23987437-23987453 chr3:23987380-23987389 chr3:23987827-23987836 chr3:23987373-23987389 chr3:23987374-23987390 chr3:23987438-23987447
38	CREB1	chr3:23987205-23988196	GM12878	blood:	n/a	chr3:23987593-23987606
39	E2F4	chr3:23986311-23988128	K562	blood:	n/a	chr3:23987157-23987167 chr3:23987154-23987164 chr3:23986821-23986830 chr3:23987440-23987450 chr3:23987783-23987793 chr3:23986932-23986941 chr3:23987372-23987381 chr3:23986483-23986490 chr3:23986479-23986491 chr3:23987442-23987451 chr3:23986483-23986490 chr3:23987437-23987447 chr3:23986483-23986490 chr3:23987446-23987455
40	POLR2A	chr3:23987148-23988265	K562	blood:	n/a	n/a
41	MYC	chr3:23985630-23988292	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23985779-23985795 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
42	SIN3AK20	chr3:23987188-23988047	K562	blood:	n/a	n/a
43	POLR2A	chr3:23986205-23988171	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr3:23987011-23988006	GM12878	blood:	n/a	n/a
45	RFX5	chr3:23987233-23988280	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr3:23986095-23988262	H1-neurons	neurons:	n/a	n/a
47	NR3C1	chr3:23987171-23987866	A549	lung:	n/a	n/a
48	MAX	chr3:23986318-23988246	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
49	CREB1	chr3:23987211-23987718	A549	lung:	n/a	chr3:23987593-23987606
50	POLR2A	chr3:23987115-23988167	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23849969..23852479-chr3:23986397..23988332,3	K562	blood:
2	chr15:78422464..78425441-chr3:23985742..23987944,2	MCF-7	breast:
3	chr3:23986774..23987327-chr5:1523908..1524413,2	Hela-S3	cervix:
4	chr3:23846531..23848270-chr3:23987055..23988984,2	MCF-7	breast:
5	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
6	chr3:23986158..23988420-chr3:24004373..24006448,3	MCF-7	breast:
7	chr3:23987103..23988093-chr6:56911476..56911991,2	Hela-S3	cervix:
8	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
9	chr3:23985869..23987641-chr3:24536460..24539004,2	MCF-7	breast:
10	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
NR1D2	TF binding region
ENSG00000174738	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000136425	Chromatin interaction
ENSG00000153395	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000166411	Chromatin interaction
ENSG00000168116	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13087250	0.82[AMR][1000 genomes]
rs13317815	0.92[AMR][1000 genomes]
rs13321439	0.92[AMR][1000 genomes]
rs13321440	0.92[AMR][1000 genomes]
rs34058540	0.83[AMR][1000 genomes]
rs34593533	0.92[AMR][1000 genomes]
rs35457462	0.88[AMR][1000 genomes]
rs36089963	0.83[AMR][1000 genomes]
rs3935253	0.82[AMR][1000 genomes]
rs4131404	0.83[AMR][1000 genomes]
rs4858096	0.83[AMR][1000 genomes]
rs4858564	0.82[AMR][1000 genomes]
rs6770052	0.94[AMR][1000 genomes]
rs6778577	0.94[AMR][1000 genomes]
rs6803587	0.94[AMR][1000 genomes]
rs73150266	0.83[AMR][1000 genomes]
rs9817923	0.83[AMR][1000 genomes]
rs9855481	0.83[AMR][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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
3	esv3449153	chr3:23984948-23988646	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3406325	chr3:23985473-23988321	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	esv3425301	chr3:23985548-23988496	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72627094	RPL15	cis	intralobular white matter	BrainEAC

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23985600-23988200	Active TSS	Fetal Kidney	kidney
2	chr3:23985600-23988400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:23985600-23988800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr3:23985800-23987600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:23985800-23987800	Active TSS	Colonic Mucosa	Colon
6	chr3:23985800-23988000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr3:23985800-23988000	Active TSS	Brain Substantia Nigra	brain
8	chr3:23985800-23988200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:23985800-23988200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:23985800-23988200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:23985800-23988200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr3:23985800-23988200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:23985800-23988200	Active TSS	Lung	lung
14	chr3:23985800-23988400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:23985800-23988400	Active TSS	Fetal Brain Female	brain
16	chr3:23985800-23988400	Active TSS	Psoas Muscle	Psoas
17	chr3:23985800-23988600	Active TSS	Brain Anterior Caudate	brain
18	chr3:23985800-23988800	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr3:23986000-23987800	Active TSS	Fetal Muscle Trunk	muscle
20	chr3:23986000-23988000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:23986000-23988000	Active TSS	Left Ventricle	heart
22	chr3:23986000-23988000	Active TSS	NHEK	skin
23	chr3:23986000-23988200	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:23986000-23988200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:23986000-23988200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:23986000-23988200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:23986000-23988200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:23986000-23988200	Active TSS	Colon Smooth Muscle	Colon
29	chr3:23986000-23988200	Active TSS	Placenta Amnion	Placenta Amnion
30	chr3:23986000-23988400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:23986000-23988400	Active TSS	Right Ventricle	heart
32	chr3:23986000-23988600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:23986000-23988600	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr3:23986000-23988600	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr3:23986000-23988800	Active TSS	Aorta	Aorta
36	chr3:23986000-23988800	Active TSS	Ovary	ovary
37	chr3:23986200-23987600	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr3:23986200-23987800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:23986200-23987800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:23986200-23987800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:23986200-23987800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr3:23986200-23987800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr3:23986200-23987800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:23986200-23987800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr3:23986200-23987800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:23986200-23987800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:23986200-23987800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr3:23986200-23987800	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr3:23986200-23987800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:23986200-23987800	Active TSS	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links