Variant report

Variant	rs12911254
Chromosome Location	chr15:75166335-75166336
allele	A/G
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	EGR1	chr15:75166180-75166421	K562	blood:	n/a	chr15:75166369-75166378 chr15:75166373-75166383 chr15:75166367-75166381 chr15:75166368-75166381 chr15:75166368-75166378 chr15:75166366-75166376 chr15:75166368-75166381 chr15:75166367-75166382 chr15:75166372-75166382 chr15:75166368-75166381 chr15:75166368-75166381
2	YY1	chr15:75166234-75166385	K562	blood:	n/a	chr15:75166373-75166382 chr15:75166367-75166376 chr15:75166370-75166381 chr15:75166370-75166379
3	EGR1	chr15:75166243-75166517	K562	blood:	n/a	chr15:75166369-75166378 chr15:75166373-75166383 chr15:75166367-75166381 chr15:75166368-75166381 chr15:75166368-75166378 chr15:75166366-75166376 chr15:75166368-75166381 chr15:75166367-75166382 chr15:75166372-75166382 chr15:75166368-75166381 chr15:75166368-75166381
4	MAX	chr15:75164982-75166402	K562	blood:	n/a	n/a
5	POLR2A	chr15:75165144-75166371	K562	blood:	n/a	n/a
6	NR2F2	chr15:75165203-75166429	K562	blood:	n/a	n/a
7	SIN3AK20	chr15:75164946-75166533	MCF-7	breast:	n/a	n/a
8	SIN3A	chr15:75165004-75166344	H1-hESC	embryonic stem cell:	n/a	n/a
9	JUND	chr15:75165294-75166399	K562	blood:	n/a	chr15:75166374-75166383
10	MAZ	chr15:75165197-75166382	K562	blood:	n/a	n/a
11	MAX	chr15:75165082-75166508	A549	lung:	n/a	n/a
12	CEBPB	chr15:75166182-75166530	K562	blood:	n/a	chr15:75166416-75166427
13	MAX	chr15:75165156-75166341	NB4	blood:	n/a	n/a
14	SMARCB1	chr15:75165153-75166366	Hela-S3	cervix:	n/a	n/a
15	TCF12	chr15:75164744-75166353	A549	lung:	n/a	chr15:75164871-75164878
16	ATF3	chr15:75165780-75166374	A549	lung:	n/a	n/a
17	MTA3	chr15:75164672-75166392	GM12878	blood:	n/a	n/a
18	STAT5A	chr15:75165764-75166411	GM12878	blood:	n/a	n/a
19	ZNF263	chr15:75165858-75166578	HEK293-T-REx	kidney:	n/a	n/a
20	ZBTB7A	chr15:75166278-75166488	K562	blood:	n/a	n/a
21	ZBTB7A	chr15:75166237-75166413	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75132063..75136088-chr15:75165447..75167881,5	K562	blood:
2	chr15:75162469..75167536-chr15:75180880..75184902,6	K562	blood:
3	chr15:75164429..75167842-chr15:75196018..75198435,3	K562	blood:
4	chr15:75163901..75170368-chr15:75180139..75184021,10	K562	blood:
5	chr15:75129767..75136088-chr15:75163908..75167881,8	K562	blood:
6	chr15:75134049..75139648-chr15:75161531..75167020,13	MCF-7	breast:
7	chr15:75163351..75167012-chr15:75180238..75185061,13	MCF-7	breast:
8	chr15:75110223..75112810-chr15:75165268..75167627,2	MCF-7	breast:
9	chr15:75166310..75168984-chr15:75177329..75180043,2	MCF-7	breast:
10	chr15:75163342..75166719-chr15:75180364..75184673,7	MCF-7	breast:
11	chr15:75161914..75167776-chr15:75191644..75199761,13	MCF-7	breast:
12	chr15:75164573..75166914-chr15:75228746..75230664,2	K562	blood:

Variant related genes	Relation type
SCAMP2	TF binding region
ENSG00000178741	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000260824	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000140474	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11072511	0.88[EUR][1000 genomes]
rs11072512	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11072513	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072514	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1127796	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1130741	0.85[EUR][1000 genomes]
rs1133322	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1133323	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11630592	0.82[EUR][1000 genomes]
rs11630918	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11633472	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11638130	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11639413	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11856413	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11857695	0.91[EUR][1000 genomes]
rs12899787	0.82[EUR][1000 genomes]
rs12900662	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12901190	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12902515	0.91[EUR][1000 genomes]
rs12903205	0.89[EUR][1000 genomes]
rs12903370	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12904326	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12904897	0.84[EUR][1000 genomes]
rs12907898	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12908365	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12909335	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12912839	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12913293	0.86[EUR][1000 genomes]
rs2044157	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2415251	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4480762	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4643278	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4886608	0.89[EUR][1000 genomes]
rs4886632	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4886636	0.85[EUR][1000 genomes]
rs4886640	0.85[EUR][1000 genomes]
rs59945415	0.82[EUR][1000 genomes]
rs62029167	0.83[EUR][1000 genomes]
rs7495664	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7495739	0.86[EUR][1000 genomes]
rs7497026	0.80[EUR][1000 genomes]
rs7497393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8025447	0.85[EUR][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	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv827386	chr15:75161362-75166473	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a
3	nsv827388	chr15:75161362-75169121	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12911254	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs12911254	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs12911254	SCAMP2	cis	Whole Blood	GTEx
rs12911254	SCAMP5	cis	Artery Tibial	GTEx
rs12911254	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75164200-75166400	Active TSS	Rectal Smooth Muscle	rectum
2	chr15:75164400-75166400	Active TSS	HSMMtube	muscle
3	chr15:75164600-75166400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:75164600-75166400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr15:75164600-75166400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:75164600-75166400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr15:75164600-75166400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr15:75164600-75166400	Active TSS	Muscle Satellite Cultured Cells	--
9	chr15:75164600-75166400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:75164600-75166400	Active TSS	Brain Cingulate Gyrus	brain
11	chr15:75164600-75166400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr15:75164600-75166400	Active TSS	A549	lung
13	chr15:75164600-75166600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr15:75164800-75166400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr15:75164800-75166400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr15:75164800-75166400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:75164800-75166400	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr15:75164800-75166400	Active TSS	Stomach Mucosa	stomach
19	chr15:75164800-75166400	Active TSS	NHDF-Ad	bronchial
20	chr15:75165000-75166400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:75165000-75166400	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr15:75165000-75166400	Active TSS	Brain Anterior Caudate	brain
23	chr15:75165000-75166400	Active TSS	Brain Hippocampus Middle	brain
24	chr15:75165000-75166400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:75165000-75166400	Active TSS	Brain Substantia Nigra	brain
26	chr15:75165000-75166400	Active TSS	Colonic Mucosa	Colon
27	chr15:75165000-75166400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr15:75165000-75166400	Active TSS	Fetal Intestine Large	intestine
29	chr15:75165000-75166400	Active TSS	Fetal Kidney	kidney
30	chr15:75165000-75166400	Active TSS	Pancreas	Pancrea
31	chr15:75165000-75166400	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr15:75165200-75166400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:75165200-75166400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:75165200-75166400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:75165800-75166400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr15:75165800-75166400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr15:75165800-75166400	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr15:75165800-75166400	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr15:75165800-75166400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr15:75165800-75166400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:75165800-75166400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:75165800-75166400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:75165800-75166400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr15:75165800-75166400	Flanking Active TSS	Liver	Liver
45	chr15:75165800-75166400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr15:75165800-75166400	Flanking Active TSS	Fetal Muscle Trunk	muscle
47	chr15:75165800-75166400	Flanking Active TSS	Dnd41	blood
48	chr15:75165800-75166400	Flanking Active TSS	Hela-S3	cervix
49	chr15:75165800-75166400	Flanking Active TSS	Osteobl	bone
50	chr15:75165800-75166600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links