Variant report

Variant	rs12899062
Chromosome Location	chr15:75347641-75347642
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75346214..75349388-chr15:75495384..75499059,5	K562	blood:
2	chr15:75345292..75348855-chr15:75495155..75497587,4	K562	blood:

Variant related genes	Relation type
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11854975	0.86[EUR][1000 genomes]
rs12101482	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12148488	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12904227	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12909515	0.85[AFR][1000 genomes]
rs1867148	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1867149	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1867151	0.81[AFR][1000 genomes]
rs2083730	0.82[AFR][1000 genomes]
rs2304902	0.81[EUR][1000 genomes]
rs35078352	0.84[EUR][1000 genomes]
rs4886417	0.80[EUR][1000 genomes]
rs4886651	0.82[AFR][1000 genomes]
rs4886652	0.80[AFR][1000 genomes]
rs4886655	0.85[EUR][1000 genomes]
rs6495144	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6495150	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6495151	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67168917	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7163362	0.82[EUR][1000 genomes]
rs7163636	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7167261	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7181261	0.82[EUR][1000 genomes]
rs8039755	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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
rs12899062	SCAMP5	cis	Artery Tibial	GTEx
rs12899062	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs12899062	SCAMP5	cis	lung	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75328800-75350400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr15:75329200-75350400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:75336000-75350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:75337200-75353600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:75339600-75351800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:75340000-75350400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:75340000-75350600	Weak transcription	NH-A	brain
8	chr15:75340000-75350600	Weak transcription	Osteobl	bone
9	chr15:75340000-75353400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:75340000-75353400	Weak transcription	NHDF-Ad	bronchial
11	chr15:75340000-75360600	Weak transcription	Gastric	stomach
12	chr15:75340200-75350200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:75340200-75350400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:75340200-75350600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:75340200-75351800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr15:75340200-75353000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:75340200-75353600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:75340200-75359400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:75340400-75350200	Weak transcription	HMEC	breast
20	chr15:75340400-75353800	Weak transcription	Liver	Liver
21	chr15:75340800-75357600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:75341000-75356400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:75341200-75357800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:75341600-75350800	Weak transcription	A549	lung
25	chr15:75342000-75350200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:75342000-75350400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:75342000-75350800	Weak transcription	Dnd41	blood
28	chr15:75342000-75357200	Weak transcription	Small Intestine	intestine
29	chr15:75342200-75350400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:75342200-75350400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:75342200-75350400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:75342200-75357600	Weak transcription	Aorta	Aorta
33	chr15:75342400-75350200	Weak transcription	NHEK	skin
34	chr15:75342400-75357400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:75342600-75348000	Weak transcription	GM12878-XiMat	blood
36	chr15:75342600-75353200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:75342600-75357000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:75342600-75357600	Weak transcription	Hela-S3	cervix
39	chr15:75342600-75364800	Weak transcription	Primary T cells from cord blood	blood
40	chr15:75342800-75350400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:75342800-75350800	Weak transcription	Esophagus	oesophagus
42	chr15:75342800-75357400	Weak transcription	Thymus	Thymus
43	chr15:75342800-75361600	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:75343000-75351000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:75343000-75354000	Weak transcription	Brain Angular Gyrus	brain
46	chr15:75343000-75354600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:75343200-75357400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:75343800-75350400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:75343800-75350800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:75343800-75353600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links