Variant report

Variant	rs12585586
Chromosome Location	chr13:50277510-50277511
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50265034..50267165-chr13:50275444..50277736,2	MCF-7	breast:
2	chr13:50265534..50267262-chr13:50276925..50279118,2	K562	blood:

Variant related genes	Relation type
ENSG00000123179	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11148160	0.86[EUR][1000 genomes]
rs2897771	0.80[ASN][1000 genomes]
rs3782930	0.80[ASN][1000 genomes]
rs3809325	0.97[ASN][1000 genomes]
rs7338721	0.80[ASN][1000 genomes]
rs7982132	0.98[ASN][1000 genomes]
rs7983905	0.90[ASN][1000 genomes]
rs7983918	0.97[ASN][1000 genomes]
rs9526596	0.80[ASN][1000 genomes]
rs9535302	0.86[EUR][1000 genomes]
rs9535304	0.98[ASN][1000 genomes]
rs9535308	0.98[ASN][1000 genomes]
rs9535309	0.85[EUR][1000 genomes]
rs9535313	0.98[ASN][1000 genomes]
rs9535319	0.80[ASN][1000 genomes]
rs9535321	0.80[ASN][1000 genomes]
rs9535328	0.80[ASN][1000 genomes]
rs9562919	0.80[ASN][1000 genomes]
rs9568313	0.98[ASN][1000 genomes]
rs9568317	0.80[ASN][1000 genomes]
rs9596183	0.97[ASN][1000 genomes]
rs9596186	0.80[ASN][1000 genomes]
rs9596187	0.80[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	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12585586	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs12585586	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs12585586	EBPL	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266000-50278200	Weak transcription	Lung	lung
2	chr13:50266000-50284200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:50266200-50279200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:50266200-50279400	Weak transcription	Brain Angular Gyrus	brain
5	chr13:50266200-50279400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:50266200-50282200	Weak transcription	Brain Germinal Matrix	brain
7	chr13:50266200-50285600	Weak transcription	NHLF	lung
8	chr13:50266200-50286000	Weak transcription	Psoas Muscle	Psoas
9	chr13:50266200-50289400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr13:50266200-50289600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr13:50266200-50295200	Weak transcription	Spleen	Spleen
12	chr13:50266200-50296000	Weak transcription	K562	blood
13	chr13:50266200-50298600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:50266200-50298800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr13:50266200-50307800	Weak transcription	Gastric	stomach
16	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr13:50266400-50281400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr13:50266400-50289400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr13:50266400-50293600	Weak transcription	Colonic Mucosa	Colon
20	chr13:50266400-50295800	Weak transcription	Small Intestine	intestine
21	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
22	chr13:50266600-50279000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr13:50266800-50279000	Weak transcription	NHEK	skin
24	chr13:50266800-50279400	Weak transcription	Colon Smooth Muscle	Colon
25	chr13:50267200-50289400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr13:50270400-50286400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:50271400-50284800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr13:50271400-50286400	Strong transcription	Dnd41	blood
29	chr13:50271400-50286800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:50271600-50284400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr13:50272400-50295000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:50272400-50296000	Weak transcription	Fetal Heart	heart
33	chr13:50273200-50278800	Weak transcription	A549	lung
34	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
35	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr13:50273400-50278200	Weak transcription	Fetal Stomach	stomach
37	chr13:50274000-50277600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr13:50274000-50286600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr13:50274200-50286400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr13:50274200-50286400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr13:50275000-50278000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr13:50275000-50280400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr13:50275200-50284800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr13:50275400-50286400	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr13:50275800-50279000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr13:50275800-50279800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr13:50275800-50289200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr13:50275800-50290000	Weak transcription	Brain Substantia Nigra	brain
49	chr13:50276000-50278800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr13:50276000-50278800	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links