Variant report

Variant	rs656473
Chromosome Location	chr15:44091351-44091352
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:118)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:118 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr15:44091169-44091602	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:44090434-44094068	GM12891	blood:	n/a	n/a
3	NFIC	chr15:44090736-44091738	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:44090541-44094332	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:44090469-44094494	U87	brain:	n/a	n/a
6	POLR2A	chr15:44090434-44094516	GM12891	blood:	n/a	n/a
7	POLR2A	chr15:44091110-44091406	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:44090432-44091899	GM12892	blood:	n/a	n/a
9	MTA3	chr15:44090831-44091925	GM12878	blood:	n/a	n/a
10	MAZ	chr15:44091125-44091711	K562	blood:	n/a	n/a
11	POLR2A	chr15:44090364-44093636	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr15:44091095-44091723	MCF-7	breast:	n/a	n/a
13	POLR2A	chr15:44090553-44091856	GM12891	blood:	n/a	n/a
14	POLR2A	chr15:44091041-44091754	MCF-7	breast:	n/a	n/a
15	NFIC	chr15:44091127-44091602	GM12878	blood:	n/a	n/a
16	MYC	chr15:44091156-44091353	MCF-7	breast:	n/a	n/a
17	ZNF143	chr15:44091090-44091765	GM12878	blood:	n/a	n/a
18	NFATC1	chr15:44090467-44091975	GM12878	blood:	n/a	n/a
19	MYC	chr15:44091096-44091357	MCF-7	breast:	n/a	n/a
20	POLR2A	chr15:44086989-44094589	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr15:44083584-44094591	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOXM1	chr15:44091173-44091791	GM12878	blood:	n/a	n/a
23	FOXM1	chr15:44091020-44091866	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:44091152-44091805	Raji	blood:	n/a	n/a
25	PML	chr15:44090431-44093563	GM12878	blood:	n/a	chr15:44090782-44090790
26	TCF3	chr15:44091054-44091372	GM12878	blood:	n/a	n/a
27	HA-E2F1	chr15:44090919-44091988	MCF-7	breast:	n/a	n/a
28	POLR2A	chr15:44090417-44091858	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr15:44090518-44091449	U87	brain:	n/a	n/a
30	POU2F2	chr15:44091007-44091420	GM12891	blood:	n/a	n/a
31	EBF1	chr15:44091066-44091812	GM12878	blood:	n/a	n/a
32	EP300	chr15:44090823-44091500	T-47D	breast:	n/a	n/a
33	RUNX3	chr15:44090968-44091858	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:44090372-44093509	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr15:44090795-44091972	PFSK-1	brain:	n/a	n/a
36	EP300	chr15:44091262-44091613	GM12878	blood:	n/a	n/a
37	POU2F2	chr15:44090949-44091800	GM12878	blood:	n/a	n/a
38	POLR2A	chr15:44090913-44091700	Hela-S3	cervix:	n/a	n/a
39	PAX5	chr15:44091013-44091774	GM12878	blood:	n/a	n/a
40	EBF1	chr15:44091178-44091801	GM12878	blood:	n/a	n/a
41	BCLAF1	chr15:44091007-44091607	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:44090470-44093815	MCF10A-Er-Src	breast:	n/a	n/a
43	MTA3	chr15:44090446-44093610	GM12878	blood:	n/a	n/a
44	POLR2A	chr15:44091347-44091729	K562	blood:	n/a	n/a
45	CTCF	chr15:44091220-44091370	GM12871	blood:	n/a	n/a
46	FOXA1	chr15:44090904-44091359	HepG2	liver:	n/a	n/a
47	POLR2A	chr15:44090502-44093448	GM12892	blood:	n/a	n/a
48	POLR2A	chr15:44090585-44094370	K562	blood:	n/a	n/a
49	WRNIP1	chr15:44090972-44091408	GM12878	blood:	n/a	n/a
50	POLR2A	chr15:44090650-44093627	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:44082965..44094882-chr15:44108427..44121402,26	K562	blood:
2	chr15:44089939..44094924-chr15:44115270..44119372,7	MCF-7	breast:
3	chr15:44038791..44041212-chr15:44089540..44091517,2	MCF-7	breast:
4	chr15:44089858..44095024-chr15:44113933..44120718,10	MCF-7	breast:
5	chr15:44062113..44074982-chr15:44088756..44097846,29	MCF-7	breast:
6	chr15:44089561..44091456-chr17:44999592..45001929,2	MCF-7	breast:
7	chr15:44090570..44093330-chr8:109259431..109261884,2	MCF-7	breast:
8	chr15:44090279..44093253-chr17:26710935..26712554,2	MCF-7	breast:
9	chr15:44065227..44073214-chr15:44081584..44094479,46	MCF-7	breast:
10	chr10:8094769..8097010-chr15:44089364..44091446,2	MCF-7	breast:

No data

Variant related genes	Relation type
SERF2	TF binding region
HYPK	TF binding region
ENSG00000262560	TF binding region
SERINC4	TF binding region
ENSG00000140264	Chromatin interaction
ENSG00000243350	Chromatin interaction
ENSG00000197308	Chromatin interaction
ENSG00000107485	Chromatin interaction
ENSG00000262633	Chromatin interaction
ENSG00000140259	Chromatin interaction
ENSG00000108433	Chromatin interaction
ENSG00000104408	Chromatin interaction
ENSG00000205771	Chromatin interaction
ENSG00000092470	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000261886	Chromatin interaction
ENSG00000167004	Chromatin interaction
ENSG00000004139	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12438668	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1814540	1.00[EUR][1000 genomes]
rs2245161	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2247734	1.00[EUR][1000 genomes]
rs2264048	1.00[EUR][1000 genomes]
rs2264051	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2444031	1.00[EUR][1000 genomes]
rs2444248	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2447200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2447214	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470123	1.00[EUR][1000 genomes]
rs28537381	1.00[EUR][1000 genomes]
rs2929276	1.00[EUR][1000 genomes]
rs2930527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2930532	1.00[EUR][1000 genomes]
rs2930534	1.00[EUR][1000 genomes]
rs35093130	1.00[EUR][1000 genomes]
rs475758	1.00[EUR][1000 genomes]
rs482124	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs483165	1.00[EUR][1000 genomes]
rs4924721	1.00[EUR][1000 genomes]
rs494774	1.00[EUR][1000 genomes]
rs555252	1.00[EUR][1000 genomes]
rs559805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56329224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59083674	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs612258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs689735	1.00[EUR][1000 genomes]
rs7171948	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS 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 miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
9	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
10	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 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	chr15:44086000-44092400	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr15:44086200-44092200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:44086200-44092200	Genic enhancers	Adipose Nuclei	Adipose
4	chr15:44086800-44091400	Strong transcription	Primary hematopoietic stem cells	blood
5	chr15:44086800-44092800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:44087000-44092000	Strong transcription	Brain Germinal Matrix	brain
7	chr15:44087000-44092000	Strong transcription	Fetal Brain Female	brain
8	chr15:44087000-44092200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
9	chr15:44087200-44092000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:44087200-44092000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr15:44087400-44092200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:44087800-44091600	Strong transcription	Brain Cingulate Gyrus	brain
13	chr15:44087800-44092000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:44087800-44092200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:44087800-44092200	Weak transcription	Small Intestine	intestine
16	chr15:44087800-44092400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:44088000-44091600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:44088000-44091600	Strong transcription	Dnd41	blood
19	chr15:44088000-44092000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
20	chr15:44088000-44092200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:44088200-44091800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:44088200-44092000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:44088400-44092000	Strong transcription	Primary T cells from cord blood	blood
24	chr15:44088400-44092200	Strong transcription	NHLF	lung
25	chr15:44088400-44092800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr15:44088600-44092200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:44088800-44092000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:44088800-44092000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr15:44088800-44092000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr15:44088800-44092000	Weak transcription	Fetal Brain Male	brain
31	chr15:44088800-44092200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:44088800-44092600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:44089000-44092400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:44089200-44092200	Genic enhancers	Duodenum Mucosa	Duodenum
35	chr15:44089200-44092200	Weak transcription	Fetal Heart	heart
36	chr15:44089200-44092400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:44089200-44092600	Genic enhancers	Placenta	Placenta
38	chr15:44089400-44092200	Genic enhancers	Left Ventricle	heart
39	chr15:44089400-44092600	Genic enhancers	HepG2	liver
40	chr15:44089600-44091600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:44089600-44091600	Weak transcription	Brain Substantia Nigra	brain
42	chr15:44089600-44092000	Strong transcription	Fetal Muscle Leg	muscle
43	chr15:44089600-44092200	Weak transcription	NHEK	skin
44	chr15:44089600-44092400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:44089800-44092000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:44089800-44092400	Genic enhancers	Fetal Intestine Large	intestine
47	chr15:44089800-44092400	Enhancers	HMEC	breast
48	chr15:44090000-44091600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:44090000-44092000	Weak transcription	Primary B cells from cord blood	blood
50	chr15:44090000-44092200	Genic enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links