Variant report

Variant	rs12913293
Chromosome Location	chr15:75184458-75184459
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr15:75184420-75185267	MCF-7	breast:	n/a	n/a
2	POLR2A	chr15:75184303-75187131	HepG2	liver:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75163351..75167012-chr15:75180238..75185061,13	MCF-7	breast:
2	chr15:75167898..75170533-chr15:75183102..75184983,2	K562	blood:
3	chr15:75130141..75132356-chr15:75184160..75186177,2	K562	blood:
4	chr15:75156545..75159476-chr15:75183223..75185437,3	MCF-7	breast:
5	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
6	chr15:75127539..75130871-chr15:75182053..75185205,4	MCF-7	breast:
7	chr15:75080217..75082228-chr15:75182575..75184955,2	MCF-7	breast:
8	chr15:75081397..75085815-chr15:75182279..75185381,4	MCF-7	breast:
9	chr15:75072512..75079183-chr15:75180576..75186728,11	MCF-7	breast:
10	chr15:75162469..75167536-chr15:75180880..75184902,6	K562	blood:
11	chr15:75181107..75185393-chr15:75190667..75200295,16	MCF-7	breast:
12	chr15:75163342..75166719-chr15:75180364..75184673,7	MCF-7	breast:
13	chr15:75182085..75184679-chr15:75247604..75250598,2	MCF-7	breast:
14	chr15:75116359..75118172-chr15:75182130..75184765,2	MCF-7	breast:
15	chr15:75133950..75137156-chr15:75180779..75184661,9	MCF-7	breast:
16	chr15:75105024..75106901-chr15:75183732..75185502,2	MCF-7	breast:
17	chr15:75184447..75185329-chr15:75193714..75194464,2	MCF-7	breast:
18	chr15:75181382..75185367-chr15:75245501..75252189,8	K562	blood:

No data

Variant related genes	Relation type
MPI	TF binding region
ENSG00000140506	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000260824	Chromatin interaction
ENSG00000264386	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000140474	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11072511	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072512	0.97[EUR][1000 genomes]
rs11072513	0.83[EUR][1000 genomes]
rs11072514	0.86[EUR][1000 genomes]
rs1127796	0.98[EUR][1000 genomes]
rs1130741	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1133322	0.95[EUR][1000 genomes]
rs1133323	0.87[EUR][1000 genomes]
rs11630918	0.84[EUR][1000 genomes]
rs11633472	0.90[EUR][1000 genomes]
rs11638130	0.89[EUR][1000 genomes]
rs11639413	0.80[EUR][1000 genomes]
rs11854704	0.91[EUR][1000 genomes]
rs11856413	0.89[EUR][1000 genomes]
rs11857695	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12439641	0.84[AFR][1000 genomes]
rs12441499	0.86[AFR][1000 genomes]
rs12898539	0.88[EUR][1000 genomes]
rs12899430	0.88[EUR][1000 genomes]
rs12899787	0.93[EUR][1000 genomes]
rs12900662	0.93[EUR][1000 genomes]
rs12901190	0.85[EUR][1000 genomes]
rs12902515	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12903205	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12903370	0.86[EUR][1000 genomes]
rs12904326	0.86[EUR][1000 genomes]
rs12904897	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12907898	0.96[EUR][1000 genomes]
rs12908365	0.94[EUR][1000 genomes]
rs12909335	0.87[EUR][1000 genomes]
rs12911254	0.86[EUR][1000 genomes]
rs12912839	0.86[EUR][1000 genomes]
rs12914217	0.85[EUR][1000 genomes]
rs2044157	0.84[EUR][1000 genomes]
rs2415251	0.80[EUR][1000 genomes]
rs3935818	0.87[AFR][1000 genomes]
rs4643278	0.93[EUR][1000 genomes]
rs4886608	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886632	0.97[EUR][1000 genomes]
rs4886636	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886639	0.87[EUR][1000 genomes]
rs4886640	0.80[AFR][1000 genomes]
rs56671860	0.86[AFR][1000 genomes]
rs59945415	0.93[EUR][1000 genomes]
rs60494786	0.86[AFR][1000 genomes]
rs62029167	0.94[EUR][1000 genomes]
rs7179093	0.87[AFR][1000 genomes]
rs729263	0.86[AFR][1000 genomes]
rs7495664	0.87[EUR][1000 genomes]
rs7495739	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7497026	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7497393	0.87[EUR][1000 genomes]
rs8025447	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8032473	0.82[AFR][1000 genomes]
rs9672491	0.82[AFR][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	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	esv990390	chr15:75179300-75187945	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12913293	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs12913293	SCAMP2	cis	Esophagus Mucosa	GTEx
rs12913293	SCAMP2	cis	Whole Blood	GTEx
rs12913293	ULK3	cis	Whole Blood	GTEx
rs12913293	SCAMP5	cis	Artery Tibial	GTEx
rs12913293	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75183000-75185400	Enhancers	Stomach Mucosa	stomach
2	chr15:75183200-75184600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:75183200-75184800	Weak transcription	Brain Germinal Matrix	brain
4	chr15:75183200-75184800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:75183200-75185000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:75183200-75185000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr15:75183200-75185000	Genic enhancers	Fetal Intestine Small	intestine
8	chr15:75183200-75185000	Enhancers	Right Atrium	heart
9	chr15:75183200-75185000	Enhancers	Right Ventricle	heart
10	chr15:75183200-75185000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr15:75183200-75185200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:75183200-75185200	Enhancers	Liver	Liver
13	chr15:75183200-75185200	Enhancers	Fetal Heart	heart
14	chr15:75183200-75185400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr15:75183200-75185800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:75183200-75186200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr15:75183200-75189400	Weak transcription	Psoas Muscle	Psoas
18	chr15:75183200-75191600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:75183200-75192000	Weak transcription	Fetal Kidney	kidney
20	chr15:75183200-75192400	Weak transcription	HUVEC	blood vessel
21	chr15:75183200-75197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr15:75183400-75184600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:75183400-75184800	Weak transcription	Primary B cells from cord blood	blood
24	chr15:75183400-75184800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr15:75183400-75184800	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:75183400-75185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:75183400-75185000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:75183400-75185000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr15:75183400-75185200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:75183400-75185200	Genic enhancers	Fetal Intestine Large	intestine
31	chr15:75183400-75185200	Genic enhancers	Fetal Muscle Leg	muscle
32	chr15:75183400-75185200	Weak transcription	HSMM	muscle
33	chr15:75183400-75185400	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr15:75183400-75185600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr15:75183400-75185800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:75183400-75186000	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr15:75183400-75186200	Genic enhancers	Esophagus	oesophagus
38	chr15:75183400-75186200	Genic enhancers	Pancreas	Pancrea
39	chr15:75183400-75186200	Strong transcription	Osteobl	bone
40	chr15:75183400-75186400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:75183400-75186400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:75183400-75186400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
43	chr15:75183400-75186400	Genic enhancers	NHEK	skin
44	chr15:75183400-75192200	Weak transcription	NH-A	brain
45	chr15:75183600-75184800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:75183600-75185000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:75183600-75185200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:75183600-75185800	Genic enhancers	GM12878-XiMat	blood
49	chr15:75183600-75186000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr15:75183600-75186200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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