Variant report

Variant	rs2446421
Chromosome Location	chr15:51634255-51634256
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:51634030-51634638	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF263	chr15:51633434-51634270	HEK293-T-REx	kidney:	n/a	chr15:51633588-51633609
3	CTCF	chr15:51634140-51634290	HMEC	breast:	n/a	n/a
4	E2F6	chr15:51633514-51634680	H1-hESC	embryonic stem cell:	n/a	chr15:51633981-51633996
5	POLR2A	chr15:51633341-51634516	MCF-7	breast:	n/a	n/a
6	YY1	chr15:51633979-51634268	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr15:51634200-51634350	SAEC	small airway:	n/a	n/a
8	CTCF	chr15:51634180-51634330	HMF	breast:	n/a	n/a
9	BACH1	chr15:51633839-51634450	H1-hESC	embryonic stem cell:	n/a	n/a
10	ZNF143	chr15:51633923-51634402	H1-hESC	embryonic stem cell:	n/a	n/a
11	GATA3	chr15:51632850-51634260	MCF-7	breast:	n/a	n/a
12	GABPA	chr15:51633965-51634270	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr15:51634172-51634319	H1-hESC	embryonic stem cell:	n/a	n/a
14	CREB1	chr15:51633890-51634470	H1-hESC	embryonic stem cell:	n/a	n/a
15	MYC	chr15:51633350-51634421	MCF-7	breast:	n/a	chr15:51633425-51633436 chr15:51633425-51633436
16	E2F6	chr15:51633419-51634831	H1-hESC	embryonic stem cell:	n/a	chr15:51633981-51633996
17	MAX	chr15:51633303-51634618	H1-hESC	embryonic stem cell:	n/a	chr15:51633425-51633436 chr15:51633425-51633436
18	HDAC2	chr15:51633297-51634719	MCF-7	breast:	n/a	n/a
19	NR2F2	chr15:51633184-51634524	MCF-7	breast:	n/a	n/a
20	CREB1	chr15:51633990-51634456	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3A	chr15:51634090-51634468	H1-hESC	embryonic stem cell:	n/a	n/a
22	HA-E2F1	chr15:51633139-51634630	MCF-7	breast:	n/a	n/a
23	MAX	chr15:51633115-51634476	MCF-7	breast:	n/a	chr15:51633425-51633436 chr15:51633425-51633436
24	CTCF	chr15:51634060-51634290	HCM	heart:	n/a	n/a
25	CTCF	chr15:51634160-51634310	HEK293	kidney:	n/a	n/a
26	CTCF	chr15:51634160-51634430	GM12871	blood:	n/a	n/a
27	CTCF	chr15:51634140-51634290	AG09319	gingival:	n/a	n/a
28	MAX	chr15:51633109-51634777	MCF-7	breast:	n/a	chr15:51633425-51633436 chr15:51633425-51633436
29	CTCF	chr15:51634166-51634291	MCF-7	breast:	n/a	n/a
30	MAX	chr15:51633510-51634709	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:51634250-51634300	HCF	heart:	n/a
2	chr15:51634250-51634300	HIPEpiC	eye:	n/a
3	chr15:51634250-51634300	Jurkat	blood:	n/a
4	chr15:51634250-51634300	HMEC	breast:	n/a
5	chr15:51634250-51634300	IMR90	lung:	fetal
6	chr15:51634250-51634300	Hela-S3	cervix:	n/a
7	chr15:51634250-51634300	NB4	blood:	n/a
8	chr15:51634250-51634300	GM12891	blood:	n/a
9	chr15:51634250-51634300	NHDF-neo	bronchial:	n/a
10	chr15:51634250-51634300	ovcar-3	ovarian:	n/a
11	chr15:51634250-51634300	Caco-2	colon:	n/a
12	chr15:51634250-51634300	HL-60	blood:	n/a
13	chr15:51634250-51634300	SKMC	muscle:	n/a
14	chr15:51634250-51634300	GM12878	blood:	n/a
15	chr15:51634250-51634300	HNPCEpiC	eye:	n/a
16	chr15:51634250-51634300	GM12892	blood:	n/a
17	chr15:51634250-51634300	CMK	blood:	n/a
18	chr15:51634250-51634300	HPAEpiC	pulmonary alveolar:	n/a
19	chr15:51634250-51634300	MCF-7	breast:	n/a
20	chr15:51634250-51634300	HEK293	kidney:	embryo
21	chr15:51634250-51634300	HUVEC	blood vessel:	n/a
22	chr15:51634250-51634300	HCM	heart:	n/a
23	chr15:51634250-51634300	PrEC	prostate:	n/a
24	chr15:51634250-51634300	HepG2	liver:	n/a
25	chr15:51634250-51634300	HRPEpiC	eye:	n/a
26	chr15:51634250-51634300	SK-N-SH	brain:	n/a
27	chr15:51634250-51634300	HEEpiC	esophagus:	n/a
28	chr15:51634250-51634300	AG04450	lung:	fetal
29	chr15:51634250-51634300	AoSMC	blood vessel:	n/a
30	chr15:51634250-51634300	BJ	skin:	n/a
31	chr15:51634250-51634300	HAEpiC	amniotic membrane:	n/a
32	chr15:51634250-51634300	GM06990	blood:	n/a
33	chr15:51634250-51634300	HCPEpiC	choroid plexus:	n/a
34	chr15:51634250-51634300	HRCEpiC	kidney:	n/a
35	chr15:51634250-51634300	AG04449	skin:	fetal
36	chr15:51634250-51634300	BE2_C	brain:	n/a
37	chr15:51634250-51634300	NH-A	brain:	n/a
38	chr15:51634250-51634300	SAEC	small airway:	n/a
39	chr15:51634250-51634300	HRE	kidney:	n/a
40	chr15:51634250-51634300	A549	lung:	n/a
41	chr15:51634250-51634300	T-47D	breast:	n/a
42	chr15:51634250-51634300	GM19239	blood:	n/a
43	chr15:51634250-51634300	AG09309	skin:	n/a
44	chr15:51634250-51634300	ECC-1	luminal epithelium:	n/a
45	chr15:51634250-51634300	AG10803	skin:	n/a
46	chr15:51634250-51634300	K562	blood:	n/a
47	chr15:51634250-51634300	H1-hESC	embryonic stem cell:	embryo
48	chr15:51634250-51634300	U87	brain:	n/a
49	chr15:51634250-51634300	PANC-1	pancreas:	n/a
50	chr15:51634250-51634300	Hepatocyte	liver:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr15:51631962..51635284-chr15:51658030..51661576,5	MCF-7	breast:
2	chr15:51629923..51631751-chr15:51631879..51634512,2	MCF-7	breast:
3	chr15:51634192..51635133-chr15:51673006..51674097,3	MCF-7	breast:
4	chr15:51633614..51635996-chr15:51658332..51660020,2	MCF-7	breast:
5	chr15:51632518..51637077-chr15:51639957..51644018,8	MCF-7	breast:

No data

Variant related genes	Relation type
CYP19A1	TF binding region
CYP19A1	CpG island
ENSG00000137869	Chromatin interaction
ENSG00000259194	Chromatin interaction
ENSG00000270378	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1841128	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1902585	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2445761	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2446410	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2446416	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2446420	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2446424	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470144	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2470147	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470164	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs752760	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv904216	chr15:51631479-51739808	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51633400-51634400	Bivalent Enhancer	Liver	Liver
2	chr15:51633400-51634400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
3	chr15:51633400-51634400	Bivalent/Poised TSS	HSMMtube	muscle
4	chr15:51633400-51634800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:51633400-51635000	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr15:51633400-51635000	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr15:51633600-51634400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:51633600-51634400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:51633600-51634400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr15:51633600-51634400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr15:51633600-51634400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr15:51633600-51634400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
13	chr15:51633600-51634400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:51633600-51634400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:51633600-51634400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:51633600-51634400	Flanking Active TSS	Pancreas	Pancrea
17	chr15:51633600-51634400	Bivalent/Poised TSS	HepG2	liver
18	chr15:51633600-51634400	Flanking Bivalent TSS/Enh	HMEC	breast
19	chr15:51633600-51634400	Bivalent/Poised TSS	HSMM	muscle
20	chr15:51633600-51634600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:51633600-51634600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:51633600-51634600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:51633600-51634600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:51633600-51634600	Active TSS	Aorta	Aorta
25	chr15:51633600-51634600	Bivalent/Poised TSS	Fetal Brain Female	brain
26	chr15:51633600-51634600	Flanking Active TSS	Psoas Muscle	Psoas
27	chr15:51633600-51634600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
28	chr15:51633600-51634600	Bivalent/Poised TSS	A549	lung
29	chr15:51633600-51634600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr15:51633600-51634600	Bivalent/Poised TSS	NHEK	skin
31	chr15:51633600-51634800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
32	chr15:51633600-51635000	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr15:51633600-51635200	Active TSS	Brain Angular Gyrus	brain
34	chr15:51633600-51635200	Active TSS	Brain Hippocampus Middle	brain
35	chr15:51633600-51635200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:51633600-51635200	Active TSS	Brain Substantia Nigra	brain
37	chr15:51633600-51635800	Active TSS	Brain Cingulate Gyrus	brain
38	chr15:51633800-51634400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr15:51633800-51634400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:51633800-51634400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:51633800-51634400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
42	chr15:51633800-51634400	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
43	chr15:51633800-51634400	Flanking Active TSS	Gastric	stomach
44	chr15:51633800-51634400	Flanking Active TSS	Ovary	ovary
45	chr15:51633800-51634400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
46	chr15:51633800-51634400	Flanking Active TSS	Spleen	Spleen
47	chr15:51633800-51634400	Active TSS	NHDF-Ad	bronchial
48	chr15:51633800-51634400	Bivalent/Poised TSS	NHLF	lung
49	chr15:51633800-51634600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
50	chr15:51633800-51634600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links