Variant report

Variant	rs2819858
Chromosome Location	chr6:45396319-45396320
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45395052..45396877-chr6:45399435..45401703,2	MCF-7	breast:
2	chr6:45391180..45393282-chr6:45393319..45396759,3	K562	blood:
3	chr6:45391736..45393950-chr6:45394810..45397600,3	K562	blood:
4	chr6:45395577..45398592-chr6:45399582..45403433,4	K562	blood:
5	chr6:45389784..45393184-chr6:45394516..45396772,3	MCF-7	breast:
6	chr6:45395765..45397797-chr6:45403659..45406189,2	K562	blood:

Variant related genes	Relation type
ENSG00000124813	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1406846	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1997992	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2064630	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2224118	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2677101	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2677102	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2677108	0.86[AFR][1000 genomes]
rs2819854	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2819855	1.00[ASN][1000 genomes]
rs2819857	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819859	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71537499	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395101	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2819858	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45392200-45396400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:45392200-45400600	Weak transcription	HMEC	breast
3	chr6:45392200-45404800	Weak transcription	Brain Substantia Nigra	brain
4	chr6:45392400-45398200	Weak transcription	HSMMtube	muscle
5	chr6:45392400-45398600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr6:45392400-45400000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:45392400-45400600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:45392400-45406800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:45392600-45400600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:45392800-45399000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:45392800-45399200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:45393000-45396600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr6:45393000-45398400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:45393000-45400600	Weak transcription	NHLF	lung
15	chr6:45393400-45397600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:45393400-45398400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:45394200-45396400	Weak transcription	NH-A	brain
18	chr6:45394200-45396600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:45394200-45397000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:45394400-45398800	Enhancers	Osteobl	bone
21	chr6:45394400-45401600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:45394400-45413200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:45395000-45396800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:45395200-45396400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:45395200-45399200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:45395400-45396400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:45395400-45396800	Enhancers	Dnd41	blood
28	chr6:45395400-45397400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr6:45395600-45396400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr6:45395600-45398600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:45395800-45396400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:45395800-45396400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:45395800-45397200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr6:45395800-45397400	Enhancers	Primary hematopoietic stem cells	blood
35	chr6:45396000-45396800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr6:45396000-45397000	Enhancers	Primary T cells from cord blood	blood
37	chr6:45396000-45397800	Strong transcription	HSMM	muscle
38	chr6:45396000-45400400	Weak transcription	NHDF-Ad	bronchial
39	chr6:45396200-45396400	Genic enhancers	Muscle Satellite Cultured Cells	--
40	chr6:45396200-45396400	Enhancers	Duodenum Mucosa	Duodenum
41	chr6:45396200-45396800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:45396200-45396800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:45396200-45397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:45396200-45398400	Weak transcription	Fetal Thymus	thymus

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