Variant report

Variant	rs12592590
Chromosome Location	chr15:56287141-56287142
allele	A/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	chr15:56287008-56287328	Hela-S3	cervix:	n/a	n/a
2	RPC155	chr15:56286572-56287271	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr15:56285035-56287150	Hela-S3	cervix:	n/a	chr15:56286825-56286838 chr15:56286689-56286697
4	FOS	chr15:56286866-56287144	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr15:56286892-56287148	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr15:56284789-56287154	Hela-S3	cervix:	n/a	n/a
7	STAT3	chr15:56286598-56287148	MCF10A-Er-Src	breast:	n/a	n/a
8	ATF1	chr15:56286965-56287213	K562	blood:	n/a	n/a
9	GTF3C2	chr15:56286339-56287245	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr15:56282393-56287197	SK-N-SH	brain:	n/a	n/a
11	JUND	chr15:56286833-56287199	K562	blood:	n/a	n/a
12	STAT3	chr15:56286155-56287141	MCF10A-Er-Src	breast:	n/a	chr15:56286309-56286317

No.	Distal block	Cell Line	Cell type
1	chr15:56285985..56288747-chr15:56326549..56330061,4	MCF-7	breast:
2	chr15:56286939..56288503-chr15:56293657..56295210,2	K562	blood:
3	chr15:56285499..56287418-chr15:56534884..56536553,2	K562	blood:
4	chr15:56284455..56287261-chr15:56299264..56302045,2	MCF-7	breast:
5	chr15:56282050..56287467-chr15:56534024..56538662,8	MCF-7	breast:

Variant related genes	Relation type
NEDD4	TF binding region
ENSG00000181827	Chromatin interaction
ENSG00000230183	Chromatin interaction
ENSG00000151575	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12101804	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12591370	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12594889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12595514	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12595614	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16976668	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1818376	0.97[ASN][1000 genomes]
rs2036742	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2036743	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28430908	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28523546	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28538091	0.83[ASN][1000 genomes]
rs28547401	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28870777	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28884883	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5007873	0.94[ASN][1000 genomes]
rs7162872	0.92[ASN][1000 genomes]
rs7183768	0.83[ASN][1000 genomes]
rs8023940	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8031535	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8035281	0.81[AFR][1000 genomes];0.82[AMR][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	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904245	chr15:56229760-56324451	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv457159	chr15:56255774-56321854	Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv569543	chr15:56255774-56321854	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv457160	chr15:56273446-56320235	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
6	nsv569544	chr15:56273446-56320235	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
7	nsv457161	chr15:56274443-56324451	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers 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	17 gene(s)	inside rSNPs	n/a
8	nsv569545	chr15:56274443-56324451	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
9	nsv569546	chr15:56274443-56337527	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56284200-56287200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr15:56285000-56287200	Active TSS	K562	blood
3	chr15:56285800-56287200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:56286200-56287200	Enhancers	Spleen	Spleen
5	chr15:56286400-56287400	Flanking Active TSS	NHEK	skin
6	chr15:56286600-56287200	Flanking Active TSS	Hela-S3	cervix
7	chr15:56286600-56287600	Enhancers	Placenta Amnion	Placenta Amnion
8	chr15:56286600-56289200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:56286600-56289200	Weak transcription	Left Ventricle	heart
10	chr15:56286600-56292000	Weak transcription	Esophagus	oesophagus
11	chr15:56286800-56287200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:56286800-56287200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:56286800-56287200	Enhancers	Fetal Intestine Large	intestine
14	chr15:56286800-56287200	Enhancers	Fetal Muscle Trunk	muscle
15	chr15:56286800-56287200	Enhancers	Pancreas	Pancrea
16	chr15:56286800-56287200	Enhancers	Right Ventricle	heart
17	chr15:56286800-56287200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr15:56286800-56287200	Enhancers	HSMMtube	muscle
19	chr15:56286800-56287400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:56286800-56289000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:56286800-56290400	Weak transcription	Psoas Muscle	Psoas
22	chr15:56287000-56287200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:56287000-56287200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:56287000-56287200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:56287000-56287200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:56287000-56287200	Flanking Active TSS	Placenta	Placenta
27	chr15:56287000-56287200	Enhancers	HMEC	breast
28	chr15:56287000-56287400	Enhancers	Fetal Intestine Small	intestine
29	chr15:56287000-56287400	Enhancers	Stomach Smooth Muscle	stomach
30	chr15:56287000-56288000	Enhancers	A549	lung
31	chr15:56287000-56289400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr15:56287000-56291600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:56287000-56291800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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