Variant report

Variant	rs1867148
Chromosome Location	chr15:75339985-75339986
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	BRCA1	chr15:75339406-75340324	GM12878	blood:	n/a	n/a
2	BHLHE40	chr15:75339151-75340243	K562	blood:	n/a	n/a
3	SPI1	chr15:75339395-75340178	GM12878	blood:	n/a	chr15:75339602-75339609 chr15:75339599-75339612 chr15:75339601-75339610
4	PML	chr15:75338604-75340440	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:75334181-75340414	GM12878	blood:	n/a	n/a
6	CHD1	chr15:75339358-75340297	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:75339540-75340083	K562	blood:	n/a	n/a
8	IRF4	chr15:75339135-75340065	GM12878	blood:	n/a	n/a
9	RELA	chr15:75339260-75340400	GM18951	blood:	n/a	n/a
10	TAF1	chr15:75339241-75340094	GM12878	blood:	n/a	n/a
11	FOXP2	chr15:75339463-75340091	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr15:75333297-75341736	GM12878	blood:	n/a	n/a
13	NFIC	chr15:75339234-75339993	ECC-1	luminal epithelium:	n/a	chr15:75339588-75339604
14	PAX5	chr15:75339937-75340214	GM12878	blood:	n/a	n/a
15	PAX5	chr15:75339015-75340118	GM12878	blood:	n/a	chr15:75339602-75339611
16	NFATC1	chr15:75339116-75340527	GM12878	blood:	n/a	n/a
17	IKZF1	chr15:75338883-75340019	GM12878	blood:	n/a	n/a
18	CUX1	chr15:75339145-75340251	GM12878	blood:	n/a	n/a
19	SPI1	chr15:75339249-75340220	GM12891	blood:	n/a	chr15:75339602-75339609 chr15:75339599-75339612 chr15:75339601-75339610
20	EP300	chr15:75339235-75340189	GM12878	blood:	n/a	chr15:75339678-75339692 chr15:75339601-75339610 chr15:75339600-75339614
21	NFIC	chr15:75338751-75340705	GM12878	blood:	n/a	chr15:75339588-75339604
22	TCF12	chr15:75339045-75340035	GM12878	blood:	n/a	n/a
23	MAX	chr15:75338937-75340297	GM12878	blood:	n/a	chr15:75339681-75339690
24	POLR2A	chr15:75338511-75340051	HL-60	blood:	n/a	n/a
25	ATF2	chr15:75339118-75340468	GM12878	blood:	n/a	n/a
26	STAT5A	chr15:75338424-75340475	GM12878	blood:	n/a	chr15:75339724-75339732 chr15:75338882-75338893 chr15:75339300-75339312 chr15:75339725-75339737
27	RELA	chr15:75339155-75340299	GM19193	blood:	n/a	n/a
28	POLR2A	chr15:75339639-75340004	HUVEC	blood vessel:	n/a	n/a
29	RELA	chr15:75339201-75340218	GM19099	blood:	n/a	n/a
30	SPI1	chr15:75339346-75340334	HL-60	blood:	n/a	chr15:75339602-75339609 chr15:75339599-75339612 chr15:75339601-75339610
31	POLR2A	chr15:75339293-75340111	PFSK-1	brain:	n/a	n/a
32	RUNX3	chr15:75338777-75340361	GM12878	blood:	n/a	n/a
33	ATF2	chr15:75339021-75340557	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:75338409-75340378	GM12878	blood:	n/a	n/a
35	POU2F2	chr15:75339018-75340835	GM12878	blood:	n/a	n/a
36	CEBPB	chr15:75339048-75340236	GM12878	blood:	n/a	n/a
37	SPI1	chr15:75339345-75340228	GM12891	blood:	n/a	chr15:75339602-75339609 chr15:75339599-75339612 chr15:75339601-75339610
38	RUNX3	chr15:75338919-75340485	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:75338823-75340239	HepG2	liver:	n/a	n/a
40	MTA3	chr15:75338784-75340743	GM12878	blood:	n/a	n/a
41	CHD2	chr15:75339180-75340223	GM12878	blood:	n/a	n/a
42	RAD21	chr15:75339142-75340318	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:75338431-75340271	GM12891	blood:	n/a	n/a
44	SPI1	chr15:75339079-75340260	GM12878	blood:	n/a	chr15:75339602-75339609 chr15:75339599-75339612 chr15:75339601-75339610
45	BCLAF1	chr15:75339055-75340341	GM12878	blood:	n/a	n/a
46	POLR2A	chr15:75338910-75340417	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:75338408-75340455	GM12892	blood:	n/a	n/a
48	BCL3	chr15:75339093-75340194	GM12878	blood:	n/a	n/a
49	FOXM1	chr15:75339008-75340310	GM12878	blood:	n/a	n/a
50	POLR2A	chr15:75338579-75340452	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75333855..75341122-chr15:75492635..75495814,9	MCF-7	breast:
2	chr15:75338159..75340815-chr15:75340871..75343132,3	MCF-7	breast:
3	chr15:75334694..75336730-chr15:75338711..75340960,2	MCF-7	breast:
4	chr15:75339319..75341137-chr15:75356875..75359232,2	K562	blood:
5	chr15:75328843..75331250-chr15:75338652..75340222,2	MCF-7	breast:
6	chr15:75331603..75340227-chr15:75492938..75499942,15	K562	blood:
7	chr15:75338739..75341398-chr15:75344086..75345973,2	MCF-7	breast:
8	chr15:75334055..75342899-chr15:75492444..75498798,20	K562	blood:
9	chr15:75327523..75330367-chr15:75338576..75340222,2	MCF-7	breast:
10	chr15:75332512..75342228-chr15:75491817..75496419,22	MCF-7	breast:

Variant related genes	Relation type
PPCDC	TF binding region
ENSG00000138621	Chromatin interaction
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11854975	0.86[EUR][1000 genomes]
rs12101482	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148488	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12899062	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12904227	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12909515	0.86[AFR][1000 genomes]
rs1867149	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867151	0.82[AFR][1000 genomes]
rs2083730	0.83[AFR][1000 genomes]
rs2304902	0.83[EUR][1000 genomes]
rs34582157	0.81[ASN][1000 genomes]
rs35078352	0.84[EUR][1000 genomes]
rs4886417	0.82[EUR][1000 genomes]
rs4886651	0.83[AFR][1000 genomes]
rs4886652	0.81[AFR][1000 genomes]
rs4886655	0.84[EUR][1000 genomes]
rs6495141	0.80[AFR][1000 genomes]
rs6495144	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495150	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6495151	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67168917	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7163362	0.81[EUR][1000 genomes]
rs7163636	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167261	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181261	0.82[EUR][1000 genomes]
rs8039755	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1867148	SCAMP5	cis	lung	GTEx
rs1867148	SCAMP5	cis	Artery Tibial	GTEx
rs1867148	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75318000-75341400	Weak transcription	Brain Germinal Matrix	brain
2	chr15:75328800-75350400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:75329200-75350400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:75329400-75346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:75330600-75340000	Weak transcription	NHEK	skin
6	chr15:75333600-75341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr15:75334000-75344600	Enhancers	Placenta	Placenta
8	chr15:75334200-75340400	Genic enhancers	Fetal Intestine Small	intestine
9	chr15:75334200-75340600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:75334200-75344600	Enhancers	Right Ventricle	heart
11	chr15:75334400-75343200	Enhancers	Fetal Heart	heart
12	chr15:75334600-75340400	Enhancers	Liver	Liver
13	chr15:75334600-75340800	Enhancers	Fetal Muscle Leg	muscle
14	chr15:75334600-75341000	Enhancers	Lung	lung
15	chr15:75334600-75343200	Enhancers	Right Atrium	heart
16	chr15:75334800-75344600	Enhancers	Left Ventricle	heart
17	chr15:75335000-75340200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr15:75335000-75340400	Enhancers	Fetal Thymus	thymus
19	chr15:75335200-75340200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:75335200-75344200	Enhancers	Fetal Lung	lung
21	chr15:75335600-75340400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr15:75335800-75340600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr15:75336000-75340200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:75336000-75350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:75336400-75340600	Enhancers	Primary hematopoietic stem cells	blood
26	chr15:75336600-75340200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:75336600-75340600	Enhancers	Small Intestine	intestine
28	chr15:75336600-75343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:75336800-75340400	Enhancers	Brain Substantia Nigra	brain
30	chr15:75336800-75340600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:75336800-75341200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr15:75336800-75342400	Enhancers	Brain Cingulate Gyrus	brain
33	chr15:75336800-75342600	Strong transcription	Primary T cells from cord blood	blood
34	chr15:75337200-75353600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:75337400-75340800	Enhancers	Spleen	Spleen
36	chr15:75337600-75340600	Weak transcription	Dnd41	blood
37	chr15:75337600-75341000	Weak transcription	Fetal Brain Female	brain
38	chr15:75337800-75340000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:75337800-75340000	Enhancers	Gastric	stomach
40	chr15:75337800-75340600	Enhancers	Primary B cells from peripheral blood	blood
41	chr15:75337800-75341000	Enhancers	Fetal Muscle Trunk	muscle
42	chr15:75338000-75340400	Enhancers	Fetal Intestine Large	intestine
43	chr15:75338000-75341800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr15:75338400-75340800	Enhancers	Stomach Mucosa	stomach
45	chr15:75338400-75342000	Genic enhancers	Esophagus	oesophagus
46	chr15:75338400-75342800	Enhancers	Brain Hippocampus Middle	brain
47	chr15:75338600-75340000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:75338600-75340200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr15:75338600-75340200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:75338600-75340400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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