Variant report

Variant	rs1648299
Chromosome Location	chr15:45491394-45491395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:228)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:228 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:45490595-45491439	H1-hESC	embryonic stem cell:	n/a	n/a
2	RCOR1	chr15:45490565-45491522	K562	blood:	n/a	n/a
3	REST	chr15:45490557-45491538	H1-neurons	neurons:	n/a	chr15:45491453-45491466
4	EBF1	chr15:45490683-45491564	GM12878	blood:	n/a	chr15:45491213-45491224
5	RAD21	chr15:45491043-45491422	HepG2	liver:	n/a	n/a
6	MAZ	chr15:45490572-45491402	HepG2	liver:	n/a	n/a
7	MAX	chr15:45490552-45491947	K562	blood:	n/a	chr15:45491480-45491489 chr15:45491479-45491490
8	POLR2A	chr15:45490610-45491924	Raji	blood:	n/a	n/a
9	POLR2A	chr15:45490716-45491911	GM12878	blood:	n/a	n/a
10	MTA3	chr15:45490468-45491434	GM12878	blood:	n/a	n/a
11	CEBPB	chr15:45490444-45491916	Hela-S3	cervix:	n/a	chr15:45490593-45490605
12	POLR2A	chr15:45490775-45491597	GM18951	blood:	n/a	n/a
13	POLR2A	chr15:45490630-45491708	GM12878	blood:	n/a	n/a
14	SIN3AK20	chr15:45491011-45491778	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr15:45490525-45491736	GM12892	blood:	n/a	n/a
16	ELF1	chr15:45490750-45491599	K562	blood:	n/a	n/a
17	POLR2A	chr15:45490509-45491493	GM12891	blood:	n/a	n/a
18	CTCF	chr15:45490453-45491461	IMR90	lung:	n/a	n/a
19	POLR2A	chr15:45490764-45491635	GM15510	blood:	n/a	n/a
20	WRNIP1	chr15:45490574-45491912	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:45490737-45491512	GM12878	blood:	n/a	n/a
22	CTCF	chr15:45490292-45491606	A549	lung:	n/a	n/a
23	NFIC	chr15:45490395-45491563	GM12878	blood:	n/a	n/a
24	TAF1	chr15:45490621-45491405	Hela-S3	cervix:	n/a	n/a
25	GTF3C2	chr15:45490270-45491914	K562	blood:	n/a	n/a
26	POLR2A	chr15:45490696-45491497	HL-60	blood:	n/a	n/a
27	ZMIZ1	chr15:45490527-45491524	K562	blood:	n/a	n/a
28	CREB1	chr15:45490605-45491446	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr15:45490413-45491461	K562	blood:	n/a	n/a
30	CHD2	chr15:45490522-45491397	K562	blood:	n/a	n/a
31	MAZ	chr15:45490420-45491965	GM12878	blood:	n/a	chr15:45491480-45491489 chr15:45491479-45491490
32	ELK1	chr15:45490601-45491568	GM12878	blood:	n/a	n/a
33	RCOR1	chr15:45490389-45491564	GM12878	blood:	n/a	n/a
34	RAD21	chr15:45490758-45491403	SK-N-SH_RA	brain:	n/a	n/a
35	CTCF	chr15:45491340-45491490	A549	lung:	n/a	n/a
36	CTCF	chr15:45491077-45491399	MCF-7	breast:	n/a	n/a
37	RUNX3	chr15:45490428-45491522	GM12878	blood:	n/a	n/a
38	MAX	chr15:45491304-45491605	HepG2	liver:	n/a	chr15:45491480-45491489 chr15:45491479-45491490
39	MXI1	chr15:45490591-45491562	HepG2	liver:	n/a	n/a
40	POLR2A	chr15:45490319-45492044	H1-neurons	neurons:	n/a	n/a
41	STAT5A	chr15:45490462-45491436	K562	blood:	n/a	n/a
42	YY1	chr15:45490279-45491739	GM12892	blood:	n/a	n/a
43	RAD21	chr15:45490466-45491420	IMR90	lung:	n/a	n/a
44	CTCF	chr15:45490971-45491464	GM10266	blood:	n/a	n/a
45	POLR2A	chr15:45490732-45491917	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr15:45491051-45491402	MCF-7	breast:	n/a	n/a
47	MAX	chr15:45490581-45491415	K562	blood:	n/a	n/a
48	FOXM1	chr15:45490399-45491436	GM12878	blood:	n/a	n/a
49	ZNF143	chr15:45490537-45491446	K562	blood:	n/a	chr15:45490878-45490896
50	TAF1	chr15:45490821-45491589	H1-neurons	neurons:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45478077..45482452-chr15:45491020..45494377,5	MCF-7	breast:
2	chr15:45490877..45493855-chr15:45879081..45881062,2	K562	blood:
3	chr15:45457346..45461990-chr15:45488766..45494297,11	MCF-7	breast:
4	chr15:45477456..45480320-chr15:45491100..45493481,2	MCF-7	breast:
5	chr15:45458639..45463256-chr15:45489443..45493548,9	K562	blood:
6	chr15:45491292..45493253-chr15:45693461..45696308,4	K562	blood:
7	chr1:226250333..226250903-chr15:45490663..45491581,2	Hela-S3	cervix:
8	chr15:45491035..45492770-chr15:45505625..45508217,2	K562	blood:
9	chr15:45490733..45493253-chr15:45692978..45696308,3	K562	blood:
10	chr15:45457899..45460285-chr15:45489261..45492223,4	MCF-7	breast:
11	chr15:45472426..45475821-chr15:45489773..45493159,3	K562	blood:
12	chr15:45457999..45463256-chr15:45488727..45493013,8	K562	blood:
13	chr15:45472971..45475470-chr15:45491028..45492942,2	MCF-7	breast:
14	chr15:45489573..45492565-chr15:45693942..45696435,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259932	TF binding region
ENSG00000259338	Chromatin interaction
ENSG00000104164	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000260170	Chromatin interaction
ENSG00000259519	Chromatin interaction
ENSG00000259539	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000261709	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000171766	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10450971	0.94[ASN][1000 genomes]
rs12440127	0.94[ASN][1000 genomes]
rs12898733	0.92[ASN][1000 genomes]
rs1611896	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1617207	0.89[ASN][1000 genomes]
rs1625404	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1625779	0.91[ASN][1000 genomes]
rs1628717	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632144	0.91[ASN][1000 genomes]
rs1648280	0.98[ASN][1000 genomes]
rs1648284	0.92[ASN][1000 genomes]
rs1648288	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648290	0.91[ASN][1000 genomes]
rs1648291	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648292	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1648296	0.92[ASN][1000 genomes]
rs1648297	0.83[ASN][1000 genomes]
rs1648298	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1648300	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648301	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648314	0.91[ASN][1000 genomes]
rs1648315	0.90[ASN][1000 genomes]
rs1706819	0.91[ASN][1000 genomes]
rs1706823	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1706828	0.98[ASN][1000 genomes]
rs1706833	0.97[ASN][1000 genomes]
rs1706836	0.97[ASN][1000 genomes]
rs2413777	0.94[ASN][1000 genomes]
rs2458238	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2458240	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458241	0.97[ASN][1000 genomes]
rs2467839	0.91[ASN][1000 genomes]
rs2668738	0.93[ASN][1000 genomes]
rs2668750	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899376	0.94[ASN][1000 genomes]
rs2899377	0.94[ASN][1000 genomes]
rs4775824	0.94[ASN][1000 genomes]
rs58701250	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167481	0.94[ASN][1000 genomes]
rs732622	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs938130	0.91[ASN][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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer 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	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 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	chr15:45489600-45494000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:45489800-45491600	Active TSS	Fetal Intestine Small	intestine
3	chr15:45489800-45493400	Active TSS	A549	lung
4	chr15:45489800-45493600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr15:45489800-45493600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr15:45489800-45493800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:45489800-45493800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr15:45489800-45493800	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr15:45489800-45494000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:45490000-45491400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:45490000-45491400	Active TSS	Primary T cells from cord blood	blood
12	chr15:45490000-45491400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:45490000-45491400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:45490000-45491400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:45490000-45491400	Active TSS	Adipose Nuclei	Adipose
16	chr15:45490000-45491400	Active TSS	Brain Germinal Matrix	brain
17	chr15:45490000-45491400	Active TSS	Stomach Smooth Muscle	stomach
18	chr15:45490000-45491600	Active TSS	Fetal Intestine Large	intestine
19	chr15:45490000-45491600	Active TSS	Fetal Stomach	stomach
20	chr15:45490000-45493600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:45490000-45493600	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr15:45490000-45493600	Active TSS	Fetal Lung	lung
23	chr15:45490000-45493800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:45490000-45493800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr15:45490000-45493800	Active TSS	Brain Anterior Caudate	brain
26	chr15:45490000-45493800	Active TSS	Fetal Kidney	kidney
27	chr15:45490000-45493800	Active TSS	K562	blood
28	chr15:45490000-45494000	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr15:45490200-45491400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:45490200-45491400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:45490200-45491400	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr15:45490200-45491400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr15:45490200-45491400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:45490200-45491400	Active TSS	Placenta	Placenta
35	chr15:45490200-45491400	Active TSS	Hela-S3	cervix
36	chr15:45490200-45491400	Active TSS	HUVEC	blood vessel
37	chr15:45490200-45491400	Active TSS	NHLF	lung
38	chr15:45490200-45491400	Active TSS	Osteobl	bone
39	chr15:45490200-45491600	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr15:45490200-45491600	Active TSS	Thymus	Thymus
41	chr15:45490200-45492200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:45490200-45493400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr15:45490200-45493400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:45490200-45493400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:45490200-45493400	Active TSS	Aorta	Aorta
46	chr15:45490200-45493400	Active TSS	Ovary	ovary
47	chr15:45490200-45493400	Active TSS	Psoas Muscle	Psoas
48	chr15:45490200-45493600	Active TSS	H1 Cell Line	embryonic stem cell
49	chr15:45490200-45493600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:45490200-45493600	Active TSS	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links