Variant report

Variant	rs2959852
Chromosome Location	chr15:76351704-76351705
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:128)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:128 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr15:76350999-76352038	SK-N-SH	brain:	n/a	chr15:76351700-76351712
2	CTCF	chr15:76351560-76351710	HCPEpiC	choroid plexus:	n/a	n/a
3	CTCF	chr15:76351640-76351790	HUVEC	blood vessel:	n/a	n/a
4	JUND	chr15:76351215-76351868	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr15:76351680-76351830	BE2_C	brain:	n/a	n/a
6	MAZ	chr15:76351654-76351797	HepG2	liver:	n/a	n/a
7	EBF1	chr15:76351522-76352117	GM12878	blood:	n/a	n/a
8	ZBTB7A	chr15:76351538-76352632	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr15:76351560-76351710	GM12867	blood:	n/a	n/a
10	MTA3	chr15:76351135-76352038	GM12878	blood:	n/a	n/a
11	CTCF	chr15:76351700-76351850	HFF-Myc	foreskin:	n/a	n/a
12	MYC	chr15:76351207-76351852	NB4	blood:	n/a	n/a
13	CTCF	chr15:76351700-76351850	HCM	heart:	n/a	n/a
14	CTCF	chr15:76351700-76351850	NB4	blood:	n/a	n/a
15	CTCF	chr15:76351580-76351730	GM12878	blood:	n/a	n/a
16	CTCF	chr15:76351620-76351770	BJ	skin:	n/a	n/a
17	SIN3A	chr15:76351262-76352755	H1-hESC	embryonic stem cell:	n/a	chr15:76352370-76352383 chr15:76352552-76352561 chr15:76352712-76352723
18	CHD2	chr15:76351696-76351840	HepG2	liver:	n/a	n/a
19	CTCF	chr15:76351601-76351817	GM19238	blood:	n/a	n/a
20	CTCF	chr15:76351626-76351801	MCF-7	breast:	n/a	n/a
21	CTCF	chr15:76351640-76351790	HBMEC	blood vessel:	n/a	n/a
22	CTCF	chr15:76351700-76351850	MCF-7	breast:	n/a	n/a
23	CTCF	chr15:76351620-76351770	AG10803	skin:	n/a	n/a
24	CTCF	chr15:76351620-76351770	HEK293	kidney:	n/a	n/a
25	CTCF	chr15:76349182-76352137	A549	lung:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349476-76349484 chr15:76349960-76349981 chr15:76349958-76349976
26	CTCF	chr15:76351600-76351750	GM12874	blood:	n/a	n/a
27	CTCF	chr15:76351640-76351790	GM12865	blood:	n/a	n/a
28	ZNF143	chr15:76351340-76351892	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr15:76351054-76351784	HCT-116	colon:	n/a	chr15:76351700-76351712
30	CTCF	chr15:76351620-76351770	AG04449	skin:	n/a	n/a
31	CTCF	chr15:76351614-76351732	GM19239	blood:	n/a	n/a
32	CTCF	chr15:76351580-76351730	AG09319	gingival:	n/a	n/a
33	RAD21	chr15:76351201-76351886	H1-hESC	embryonic stem cell:	n/a	chr15:76351700-76351712
34	MXI1	chr15:76351704-76351865	GM12878	blood:	n/a	n/a
35	CTCF	chr15:76351560-76351710	HA-sp	spinal cord:	n/a	n/a
36	CTCF	chr15:76351620-76351770	HCFaa	heart:	n/a	n/a
37	HDAC2	chr15:76351541-76352082	H1-hESC	embryonic stem cell:	n/a	n/a
38	TBP	chr15:76351573-76351857	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr15:76351620-76351770	GM12873	blood:	n/a	n/a
40	CTCF	chr15:76351600-76351750	Caco-2	colon:	n/a	n/a
41	CTCF	chr15:76351604-76351873	MCF-7	breast:	n/a	n/a
42	CTCF	chr15:76351185-76351844	GM12878	blood:	n/a	n/a
43	CTCF	chr15:76351640-76351790	HAc	cerebellar:	n/a	n/a
44	MAX	chr15:76351568-76351803	GM12878	blood:	n/a	n/a
45	CTCF	chr15:76351600-76351750	WERI-Rb-1	eye:	n/a	n/a
46	CTCF	chr15:76351620-76351770	SK-N-SH_RA	brain:	n/a	n/a
47	CTCF	chr15:76351625-76351806	MCF-7	breast:	n/a	n/a
48	CTCF	chr15:76351660-76351810	GM12869	blood:	n/a	n/a
49	CTCF	chr15:76351700-76351850	GM12866	blood:	n/a	n/a
50	RAD21	chr15:76351232-76351781	HepG2	liver:	n/a	chr15:76351700-76351712

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:76350662..76351851-chr15:76431467..76432496,4	MCF-7	breast:
2	chr15:76351061..76352065-chr15:76400191..76401011,4	MCF-7	breast:
3	chr15:76134992..76136572-chr15:76350644..76353343,2	MCF-7	breast:
4	chr15:76195094..76197177-chr15:76350015..76352498,2	K562	blood:
5	chr15:76350898..76351807-chr15:76431306..76432503,7	MCF-7	breast:

No data

Variant related genes	Relation type
NRG4	TF binding region
C15orf27	TF binding region
ENSG00000167196	Chromatin interaction
ENSG00000140367	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12910576	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12915012	0.81[AMR][1000 genomes]
rs1695378	0.81[EUR][1000 genomes]
rs1699263	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs184580	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs189197	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2255701	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2441929	0.80[EUR][1000 genomes]
rs2455899	0.80[EUR][1000 genomes]
rs2460798	0.80[EUR][1000 genomes]
rs2469039	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2593280	0.80[EUR][1000 genomes]
rs28876229	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs334930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334934	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334936	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs335681	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs335697	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs335706	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs335711	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4886753	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4886754	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71403522	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8024155	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs985849	0.84[AMR][1000 genomes];0.93[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	nsv904398	chr15:76220285-76359055	Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1617	chr15:76332103-76359435	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1048760	chr15:76334544-76496977	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3425731	chr15:76350922-76353470	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76350400-76351800	Flanking Active TSS	GM12878-XiMat	blood
2	chr15:76350800-76353200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:76351000-76351800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
4	chr15:76351000-76351800	Flanking Bivalent TSS/Enh	NHEK	skin
5	chr15:76351000-76352000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
6	chr15:76351000-76352000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:76351000-76352000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
8	chr15:76351000-76353000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:76351000-76353000	Active TSS	Right Atrium	heart
10	chr15:76351000-76353200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr15:76351000-76353200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr15:76351200-76351800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:76351200-76351800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
14	chr15:76351200-76351800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:76351200-76351800	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr15:76351200-76351800	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr15:76351200-76351800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr15:76351200-76351800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
19	chr15:76351200-76351800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
20	chr15:76351200-76351800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
21	chr15:76351200-76351800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
22	chr15:76351200-76351800	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
23	chr15:76351200-76351800	Flanking Bivalent TSS/Enh	HSMM	muscle
24	chr15:76351200-76351800	Flanking Bivalent TSS/Enh	Osteobl	bone
25	chr15:76351200-76352000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
26	chr15:76351200-76352000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
27	chr15:76351200-76352000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
28	chr15:76351200-76352000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:76351200-76352000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
30	chr15:76351200-76352000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:76351200-76352000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:76351200-76352000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:76351200-76352000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:76351200-76352000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
35	chr15:76351200-76352000	Flanking Active TSS	HMEC	breast
36	chr15:76351200-76352600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:76351200-76352600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:76351200-76353000	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr15:76351200-76353000	Active TSS	Psoas Muscle	Psoas
40	chr15:76351200-76353200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr15:76351400-76351800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:76351400-76351800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:76351400-76351800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:76351400-76351800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
45	chr15:76351400-76351800	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
46	chr15:76351400-76351800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:76351400-76351800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr15:76351400-76351800	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
49	chr15:76351400-76351800	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
50	chr15:76351400-76351800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--

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