Variant report

Variant	rs1378941
Chromosome Location	chr15:75080150-75080151
allele	G/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	IRF4	chr15:75079607-75081355	GM12878	blood:	n/a	n/a
2	FOXM1	chr15:75079358-75081791	GM12878	blood:	n/a	n/a
3	JUND	chr15:75080125-75080450	H1-hESC	embryonic stem cell:	n/a	n/a
4	CREB1	chr15:75079691-75081604	GM12878	blood:	n/a	n/a
5	BCL3	chr15:75079694-75080568	GM12878	blood:	n/a	chr15:75080342-75080351
6	CTCF	chr15:75080030-75080441	GM12891	blood:	n/a	chr15:75080410-75080423
7	TCF12	chr15:75079723-75080458	GM12878	blood:	n/a	chr15:75080186-75080193
8	SPI1	chr15:75079235-75080757	GM12878	blood:	n/a	chr15:75080342-75080351 chr15:75080585-75080598
9	CTCF	chr15:75080122-75080381	HepG2	liver:	n/a	n/a
10	YY1	chr15:75079782-75080536	GM12891	blood:	n/a	n/a
11	FAM48A	chr15:75079924-75080214	GM12878	blood:	n/a	n/a
12	RELA	chr15:75079731-75081849	GM18526	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
13	YY1	chr15:75079609-75080553	GM12878	blood:	n/a	n/a
14	BCLAF1	chr15:75079284-75082025	GM12878	blood:	n/a	chr15:75081349-75081362 chr15:75080342-75080351
15	RAD21	chr15:75079994-75080432	H1-hESC	embryonic stem cell:	n/a	n/a
16	E2F4	chr15:75079866-75080699	GM12878	blood:	n/a	n/a
17	ETS1	chr15:75079663-75080717	GM12878	blood:	n/a	chr15:75080342-75080353 chr15:75080342-75080355 chr15:75080340-75080354
18	ZNF143	chr15:75080149-75080433	K562	blood:	n/a	n/a
19	CUX1	chr15:75080120-75080288	K562	blood:	n/a	n/a
20	KAP1	chr15:75079940-75080431	HEK293	kidney:	n/a	n/a
21	RELA	chr15:75078968-75083276	GM18951	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
22	MEF2A	chr15:75079477-75080696	GM12878	blood:	n/a	chr15:75079564-75079575 chr15:75079565-75079574
23	ATF2	chr15:75078945-75081778	GM12878	blood:	n/a	chr15:75079326-75079340
24	POLR2A	chr15:75077574-75083240	GM19193	blood:	n/a	n/a
25	NFATC1	chr15:75079098-75082965	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:75078871-75082774	GM12891	blood:	n/a	n/a
27	STAT3	chr15:75079696-75081648	GM12878	blood:	n/a	chr15:75081561-75081573
28	ZNF143	chr15:75079353-75080576	GM12878	blood:	n/a	chr15:75079454-75079472
29	POLR2A	chr15:75078541-75083313	GM12892	blood:	n/a	n/a
30	CTCF	chr15:75080137-75080396	HepG2	liver:	n/a	n/a
31	RCOR1	chr15:75079715-75080838	IMR90	lung:	n/a	n/a
32	POLR2A	chr15:75078876-75083272	GM12878	blood:	n/a	n/a
33	ZNF143	chr15:75080089-75080462	H1-hESC	embryonic stem cell:	n/a	n/a
34	ELF1	chr15:75080141-75080515	K562	blood:	n/a	chr15:75080344-75080357
35	RELA	chr15:75078928-75083342	GM18505	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
36	ZNF263	chr15:75079269-75080344	K562	blood:	n/a	chr15:75079479-75079500
37	BHLHE40	chr15:75079621-75081908	GM12878	blood:	n/a	chr15:75081355-75081371
38	RELA	chr15:75079439-75082060	GM15510	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
39	CTCF	chr15:75080127-75080404	Spleen_OC	spleen:	n/a	n/a
40	POU2F2	chr15:75078933-75083247	GM12878	blood:	n/a	chr15:75081175-75081185 chr15:75081175-75081185 chr15:75081174-75081186 chr15:75081172-75081187 chr15:75081176-75081183 chr15:75081168-75081189 chr15:75081174-75081184 chr15:75081175-75081183 chr15:75081175-75081184 chr15:75081170-75081188 chr15:75081173-75081184
41	SPI1	chr15:75079659-75080564	HL-60	blood:	n/a	chr15:75080342-75080351
42	POLR2A	chr15:75078956-75083263	GM12892	blood:	n/a	n/a
43	CHD2	chr15:75079257-75083224	GM12878	blood:	n/a	n/a
44	RAD21	chr15:75080113-75080557	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:75079535-75083264	GM12878	blood:	n/a	n/a
46	POLR2A	chr15:75080104-75080154	K562	blood:	n/a	n/a
47	POLR2A	chr15:75076731-75083396	GM12892	blood:	n/a	n/a
48	BRCA1	chr15:75079767-75081462	GM12878	blood:	n/a	n/a
49	MAX	chr15:75080123-75080389	K562	blood:	n/a	n/a
50	EGR1	chr15:75080030-75080521	GM12878	blood:	n/a	chr15:75080345-75080354 chr15:75080381-75080403 chr15:75080385-75080398

No.	Distal block	Cell Line	Cell type
1	chr15:75078437..75080336-chr15:75126473..75129418,2	MCF-7	breast:
2	chr15:75079479..75082400-chr15:75103794..75106182,2	MCF-7	breast:
3	chr15:75073170..75080511-chr15:75126432..75130376,7	MCF-7	breast:
4	chr15:75078025..75080593-chr15:75113459..75116440,2	K562	blood:
5	chr15:75078889..75080796-chr15:75108013..75111153,3	MCF-7	breast:
6	chr15:75079443..75082335-chr15:75197190..75199145,2	MCF-7	breast:
7	chr15:75078830..75080819-chr15:75135000..75137189,2	K562	blood:
8	chr15:75079215..75085047-chr15:75133215..75137478,7	MCF-7	breast:
9	chr15:74906678..74909061-chr15:75078128..75081929,4	MCF-7	breast:
10	chr15:75079725..75083728-chr15:75089989..75095483,10	MCF-7	breast:

Variant related genes	Relation type
CSK	TF binding region
ENSG00000140474	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000179335	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11072507	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11072508	0.91[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630478	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11632414	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635664	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636952	0.95[CEU][hapmap]
rs12591513	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594062	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898997	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903541	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12903896	0.87[AMR][1000 genomes]
rs12905199	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909307	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12917376	0.94[ASN][1000 genomes]
rs1378940	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1378942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470890	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2472304	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2960192	0.89[AMR][1000 genomes]
rs34862454	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35206230	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3765066	0.82[CEU][hapmap]
rs3784789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62006566	0.80[AMR][1000 genomes]
rs62006567	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1378941	SCAMP5	cis	Artery Tibial	GTEx
rs1378941	SCAMP5	cis	lung	GTEx
rs1378941	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75075600-75080800	Enhancers	Fetal Heart	heart
2	chr15:75075600-75083400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr15:75075800-75082000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr15:75076000-75080400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:75076000-75080600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:75076000-75080800	Enhancers	Fetal Brain Male	brain
7	chr15:75076200-75080200	Enhancers	Psoas Muscle	Psoas
8	chr15:75076200-75080200	Enhancers	Stomach Mucosa	stomach
9	chr15:75076400-75082200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr15:75076400-75083200	Enhancers	Colon Smooth Muscle	Colon
11	chr15:75076400-75083400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr15:75076400-75083400	Genic enhancers	Fetal Stomach	stomach
13	chr15:75076400-75083400	Enhancers	Right Ventricle	heart
14	chr15:75076400-75084200	Enhancers	Spleen	Spleen
15	chr15:75076400-75085800	Enhancers	Left Ventricle	heart
16	chr15:75076600-75080400	Enhancers	Brain Germinal Matrix	brain
17	chr15:75076600-75080800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:75076600-75080800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:75076600-75081000	Genic enhancers	Fetal Intestine Large	intestine
20	chr15:75076600-75082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:75076600-75082600	Genic enhancers	NHEK	skin
22	chr15:75076600-75082800	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr15:75076600-75083400	Enhancers	Right Atrium	heart
24	chr15:75076600-75083400	Enhancers	HMEC	breast
25	chr15:75076600-75084800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:75076800-75081600	Genic enhancers	Fetal Intestine Small	intestine
27	chr15:75076800-75083200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:75077200-75081000	Genic enhancers	K562	blood
29	chr15:75077200-75082200	Genic enhancers	Fetal Muscle Leg	muscle
30	chr15:75077600-75081800	Genic enhancers	Lung	lung
31	chr15:75077600-75083000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:75077600-75083000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:75077600-75083200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:75077800-75081200	Enhancers	Brain Substantia Nigra	brain
35	chr15:75077800-75082200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:75077800-75084400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:75077800-75092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:75078000-75080600	Weak transcription	Fetal Kidney	kidney
39	chr15:75078000-75081200	Enhancers	Liver	Liver
40	chr15:75078000-75081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:75078000-75082000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr15:75078000-75083400	Enhancers	Placenta	Placenta
43	chr15:75078000-75083400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr15:75078000-75083600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr15:75078000-75084200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr15:75078000-75085600	Enhancers	NHDF-Ad	bronchial
47	chr15:75078200-75081600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:75078200-75081600	Weak transcription	HUVEC	blood vessel
49	chr15:75078200-75082400	Enhancers	Brain Cingulate Gyrus	brain
50	chr15:75078200-75083200	Enhancers	Gastric	stomach

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