Variant report

Variant	rs2066598
Chromosome Location	chr13:50728013-50728014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50699701..50701287-chr13:50725800..50728308,2	K562	blood:
2	chr13:50727152..50729552-chr13:50729761..50732291,3	MCF-7	breast:
3	chr13:50724073..50728700-chr13:50729258..50733237,4	K562	blood:

Variant related genes	Relation type
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17073826	1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073834	0.87[EUR][1000 genomes]
rs17471092	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1963729	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066586	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2177313	0.93[CEU][hapmap]
rs61962359	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6561576	0.82[EUR][1000 genomes]
rs66559968	0.82[EUR][1000 genomes]
rs73196768	0.87[EUR][1000 genomes]
rs7325091	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7339181	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs7981648	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7986364	0.93[CEU][hapmap]
rs7991744	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7995192	1.00[JPT][hapmap]
rs7998223	0.92[CEU][hapmap]
rs9596240	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1041501	chr13:50683189-50795195	Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv900076	chr13:50710579-50912578	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2066598	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs2066598	DLEU1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50724400-50729000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:50724400-50729400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:50724400-50730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:50724400-50730400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr13:50724400-50733400	Weak transcription	Psoas Muscle	Psoas
6	chr13:50725800-50728200	Flanking Active TSS	Dnd41	blood
7	chr13:50726400-50728200	Active TSS	Brain Angular Gyrus	brain
8	chr13:50726400-50728400	Active TSS	Brain Substantia Nigra	brain
9	chr13:50726600-50728200	Active TSS	Brain Cingulate Gyrus	brain
10	chr13:50726600-50728400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr13:50726800-50730000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:50726800-50734600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:50726800-50735000	Weak transcription	NHLF	lung
14	chr13:50727000-50728200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:50727000-50728400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr13:50727000-50730200	Weak transcription	NHDF-Ad	bronchial
17	chr13:50727000-50730600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:50727000-50730600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:50727000-50732400	Weak transcription	Primary B cells from cord blood	blood
20	chr13:50727400-50728400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr13:50727400-50729800	Weak transcription	HepG2	liver
22	chr13:50727600-50728200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:50727600-50728200	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr13:50727600-50730200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr13:50727800-50730200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr13:50727800-50730600	Weak transcription	HSMM	muscle
27	chr13:50728000-50728200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr13:50728000-50730000	Weak transcription	Osteobl	bone
29	chr13:50728000-50732600	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links