Variant report

Variant	rs2677101
Chromosome Location	chr6:45398157-45398158
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45344371..45347422-chr6:45396890..45400030,4	K562	blood:
2	chr6:45395577..45398592-chr6:45399582..45403433,4	K562	blood:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1406846	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1997992	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2064630	1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2224118	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2677102	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2677108	0.82[ASW][hapmap];0.82[CHD][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2819854	0.84[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2819855	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[ASN][1000 genomes]
rs2819857	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819858	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819859	0.97[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	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472487	0.89[CEU][hapmap];0.87[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2677101	SUPT3H	cis	cerebellum	SCAN
rs2677101	SUPT3H	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45392200-45400600	Weak transcription	HMEC	breast
2	chr6:45392200-45404800	Weak transcription	Brain Substantia Nigra	brain
3	chr6:45392400-45398200	Weak transcription	HSMMtube	muscle
4	chr6:45392400-45398600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:45392400-45400000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:45392400-45400600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:45392400-45406800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:45392600-45400600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:45392800-45399000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:45392800-45399200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:45393000-45398400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:45393000-45400600	Weak transcription	NHLF	lung
13	chr6:45393400-45398400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:45394400-45398800	Enhancers	Osteobl	bone
15	chr6:45394400-45401600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:45394400-45413200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:45395200-45399200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:45395600-45398600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:45396000-45400400	Weak transcription	NHDF-Ad	bronchial
20	chr6:45396200-45398400	Weak transcription	Fetal Thymus	thymus
21	chr6:45396400-45398800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:45396400-45400000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:45396400-45400400	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr6:45396400-45401400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:45396600-45399800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr6:45396800-45399200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr6:45396800-45404200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:45397000-45398200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:45397000-45399200	Weak transcription	Primary T cells from cord blood	blood
30	chr6:45397000-45399200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:45397000-45399600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:45397200-45399400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:45397200-45400200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:45397400-45398200	Weak transcription	NH-A	brain
35	chr6:45397400-45398400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:45397400-45398400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:45397400-45398400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:45397400-45398600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:45397400-45405400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:45397800-45399000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:45397800-45402400	Genic enhancers	HSMM	muscle
42	chr6:45397800-45402800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr6:45398000-45398200	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:45398000-45399400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:45398000-45399800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:45398000-45401600	Genic enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links