Variant report

Variant	rs2664139
Chromosome Location	chr15:39872583-39872584
allele	C/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	CTCF	chr15:39872460-39872610	GM12864	blood:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
2	CTCF	chr15:39872438-39872732	GM19239	blood:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
3	CTCF	chr15:39872440-39872590	HCFaa	heart:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
4	NFIC	chr15:39871702-39872903	ECC-1	luminal epithelium:	n/a	n/a
5	TAF1	chr15:39872379-39872678	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr15:39872367-39872758	T-47D	breast:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
7	CTCF	chr15:39872480-39872630	HMEC	breast:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
8	CTCF	chr15:39872440-39872590	HMF	breast:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
9	RFX5	chr15:39872358-39872769	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr15:39872298-39872829	H1-hESC	embryonic stem cell:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
11	CTCF	chr15:39872520-39872670	HCT-116	colon:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
12	YY1	chr15:39871765-39872721	H1-hESC	embryonic stem cell:	n/a	chr15:39872660-39872674 chr15:39872654-39872668
13	CTCF	chr15:39872460-39872610	HEEpiC	esophagus:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
14	CTCF	chr15:39872480-39872630	GM12878	blood:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
15	PAX5	chr15:39872496-39872878	GM12891	blood:	n/a	n/a
16	BHLHE40	chr15:39871769-39873546	HepG2	liver:	n/a	chr15:39873437-39873453 chr15:39873434-39873450 chr15:39873397-39873413 chr15:39872593-39872609
17	CTCF	chr15:39872480-39872630	WERI-Rb-1	eye:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
18	FOXP2	chr15:39872425-39872775	PFSK-1	brain:	n/a	n/a
19	HA-E2F1	chr15:39871879-39873682	MCF-7	breast:	n/a	chr15:39872600-39872610 chr15:39873039-39873050 chr15:39872657-39872667 chr15:39873106-39873115
20	CTCF	chr15:39872480-39872630	SK-N-SH_RA	brain:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
21	MAX	chr15:39872374-39873661	HepG2	liver:	n/a	chr15:39872697-39872706 chr15:39873005-39873014
22	CTCF	chr15:39872520-39872670	NB4	blood:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
23	CEBPB	chr15:39871622-39873327	IMR90	lung:	n/a	n/a
24	CTCF	chr15:39872404-39872729	Kidney_OC	kidney:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
25	SIN3AK20	chr15:39872341-39872717	SK-N-SH	brain:	n/a	n/a
26	CHD2	chr15:39872492-39872781	HepG2	liver:	n/a	n/a
27	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
28	EBF1	chr15:39872188-39872724	GM12878	blood:	n/a	n/a
29	MAX	chr15:39872366-39872813	K562	blood:	n/a	chr15:39872697-39872706
30	CTCF	chr15:39872081-39872919	HCT-116	colon:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
31	CTCF	chr15:39872480-39872630	GM12868	blood:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
32	MAX	chr15:39871634-39873501	ECC-1	luminal epithelium:	n/a	chr15:39872697-39872706 chr15:39873005-39873014
33	TCF12	chr15:39871518-39874274	A549	lung:	n/a	chr15:39874183-39874190
34	CTCF	chr15:39872430-39872695	A549	lung:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
35	POLR2A	chr15:39872374-39882964	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr15:39872526-39874281	MCF-7	breast:	n/a	n/a
37	CTCF	chr15:39872356-39872745	SK-N-SH_RA	brain:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
38	RAD21	chr15:39871967-39873023	HCT-116	colon:	n/a	chr15:39872590-39872600 chr15:39872814-39872824 chr15:39872530-39872549
39	CTCF	chr15:39872520-39872670	HA-sp	spinal cord:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
40	CTCF	chr15:39872480-39872630	HVMF	connective:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
41	HDAC2	chr15:39872403-39873557	MCF-7	breast:	n/a	n/a
42	POLR2A	chr15:39871542-39884619	MCF10A-Er-Src	breast:	n/a	n/a
43	RCOR1	chr15:39871893-39872755	HepG2	liver:	n/a	n/a
44	EP300	chr15:39871773-39873784	SK-N-SH	brain:	n/a	chr15:39872532-39872548 chr15:39871893-39871903 chr15:39872594-39872610 chr15:39873442-39873451 chr15:39873397-39873413 chr15:39873444-39873453 chr15:39873555-39873571
45	CREB1	chr15:39871656-39872814	H1-hESC	embryonic stem cell:	n/a	n/a
46	CEBPB	chr15:39872415-39873171	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr15:39872440-39872590	HBMEC	blood vessel:	n/a	chr15:39872533-39872549 chr15:39872532-39872550
48	BHLHE40	chr15:39872369-39872642	GM12878	blood:	n/a	chr15:39872593-39872609
49	CTCF	chr15:39872308-39872733	K562	blood:	n/a	chr15:39872532-39872550 chr15:39872533-39872549
50	GATA2	chr15:39870911-39872650	HUVEC	blood vessel:	n/a	chr15:39871069-39871085 chr15:39872609-39872619 chr15:39871069-39871085 chr15:39871089-39871106

No.	Distal block	Cell Line	Cell type
1	chr15:39462462..39474613-chr15:39871091..39879136,29	MCF-7	breast:
2	chr15:39561763..39569547-chr15:39871861..39876512,9	MCF-7	breast:
3	chr15:39464364..39464897-chr15:39872073..39872634,2	K562	blood:
4	chr15:39604878..39605861-chr15:39871871..39872591,2	K562	blood:
5	chr15:39457550..39462148-chr15:39871822..39875383,4	MCF-7	breast:
6	chr15:39604961..39605804-chr15:39872140..39873022,3	MCF-7	breast:
7	chr15:39562139..39567868-chr15:39871478..39875404,11	MCF-7	breast:
8	chr15:39464246..39465494-chr15:39872336..39873186,5	MCF-7	breast:
9	chr15:39417793..39418784-chr15:39872067..39872984,4	K562	blood:
10	chr15:39735362..39737088-chr15:39871158..39872700,2	MCF-7	breast:
11	chr14:93147508..93148020-chr15:39872126..39872979,2	MCF-7	breast:

Variant related genes	Relation type
THBS1	TF binding region
ENSG00000259345	Chromatin interaction
ENSG00000259423	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10152640	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10520137	0.81[ASN][1000 genomes]
rs10520138	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070220	0.86[ASN][1000 genomes]
rs11070225	0.81[ASN][1000 genomes]
rs1134485	0.89[ASN][1000 genomes]
rs1134486	0.84[ASN][1000 genomes]
rs12443011	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12908846	0.81[ASN][1000 genomes]
rs12912082	0.92[ASN][1000 genomes]
rs1478604	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1478605	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16969386	0.81[ASN][1000 genomes]
rs16969395	0.84[ASN][1000 genomes]
rs1876852	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1904209	0.86[ASN][1000 genomes]
rs2169830	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228261	0.84[ASN][1000 genomes]
rs2229364	0.84[ASN][1000 genomes]
rs2292305	0.92[ASN][1000 genomes]
rs2411315	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2412412	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2412418	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2618162	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2618163	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2664141	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3743125	0.85[ASN][1000 genomes]
rs4319740	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66781090	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7167366	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7170682	0.90[ASN][1000 genomes]
rs7176721	0.84[AMR][1000 genomes]
rs7177324	0.81[ASN][1000 genomes]
rs7179293	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7183544	0.91[ASN][1000 genomes]
rs753598	0.87[ASN][1000 genomes]
rs753599	0.92[ASN][1000 genomes]
rs8032035	0.81[ASN][1000 genomes]
rs8034594	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8036376	0.91[ASN][1000 genomes]
rs8036633	0.91[ASN][1000 genomes]
rs8039035	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs949646	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs964424	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs970280	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9806365	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9806647	0.81[ASN][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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39871200-39872600	Enhancers	Lung	lung
2	chr15:39871400-39872600	Flanking Active TSS	NHEK	skin
3	chr15:39871400-39872800	Bivalent Enhancer	Fetal Thymus	thymus
4	chr15:39871400-39873000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr15:39871400-39873800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr15:39871600-39872600	Weak transcription	Small Intestine	intestine
7	chr15:39871600-39872800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
8	chr15:39871600-39872800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
9	chr15:39871600-39872800	Active TSS	Fetal Muscle Trunk	muscle
10	chr15:39871600-39873000	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr15:39871600-39873000	Active TSS	Stomach Smooth Muscle	stomach
12	chr15:39871600-39873400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:39871600-39873600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr15:39871600-39873600	Active TSS	Brain Angular Gyrus	brain
15	chr15:39871600-39874000	Active TSS	Ovary	ovary
16	chr15:39871600-39874200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:39871600-39875400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:39871600-39875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:39871800-39872600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr15:39871800-39872600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:39871800-39872600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:39871800-39872600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:39871800-39872600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:39871800-39872600	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr15:39871800-39872600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr15:39871800-39872800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr15:39871800-39872800	Active TSS	Right Atrium	heart
28	chr15:39871800-39872800	Bivalent/Poised TSS	Thymus	Thymus
29	chr15:39871800-39873400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr15:39871800-39873400	Active TSS	NHDF-Ad	bronchial
31	chr15:39871800-39873800	Active TSS	Esophagus	oesophagus
32	chr15:39871800-39874000	Active TSS	H9 Cell Line	embryonic stem cell
33	chr15:39871800-39874000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:39871800-39874000	Active TSS	Colon Smooth Muscle	Colon
35	chr15:39871800-39874000	Active TSS	Rectal Smooth Muscle	rectum
36	chr15:39871800-39874000	Active TSS	A549	lung
37	chr15:39871800-39874400	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr15:39871800-39874400	Active TSS	Left Ventricle	heart
39	chr15:39871800-39874400	Active TSS	Placenta Amnion	Placenta Amnion
40	chr15:39871800-39874800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:39871800-39874800	Active TSS	Fetal Kidney	kidney
42	chr15:39871800-39875200	Active TSS	Gastric	stomach
43	chr15:39872000-39872600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:39872000-39872600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr15:39872000-39872600	Active TSS	Right Ventricle	heart
46	chr15:39872000-39872600	Enhancers	Spleen	Spleen
47	chr15:39872000-39873400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:39872000-39873400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:39872000-39873400	Active TSS	Aorta	Aorta
50	chr15:39872000-39873800	Active TSS	iPS-18 Cell Line	embryonic stem cell

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