Variant report

Variant	rs2790100
Chromosome Location	chr6:45430336-45430337
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	chr6:45419819..45421341-chr6:45429918..45432276,2	K562	blood:
2	chr6:45426065..45427907-chr6:45429310..45431026,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10214519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12197948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12210100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12215249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1317777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13208741	1.00[JPT][hapmap]
rs1343799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934327	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2252718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2256819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396442	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2677098	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677100	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677109	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790094	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790095	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2790097	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790099	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790102	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819865	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819866	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2819867	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2820340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711816	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4714854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7756144	0.93[EUR][1000 genomes]
rs910586	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9472494	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9885645	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45407200-45462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:45414000-45431400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:45416400-45430600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:45416400-45440400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:45419200-45456200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:45422000-45441200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:45422000-45445000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:45422200-45440000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:45422400-45438200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr6:45422600-45432400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:45422600-45437200	Weak transcription	NHDF-Ad	bronchial
12	chr6:45422600-45439800	Weak transcription	NHLF	lung
13	chr6:45423000-45454400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:45423400-45434600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:45425600-45444000	Weak transcription	Fetal Thymus	thymus
16	chr6:45426600-45430800	Strong transcription	Dnd41	blood
17	chr6:45426800-45444200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:45428600-45430600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:45428600-45431600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:45428800-45430800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:45429000-45430800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:45429000-45430800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:45429000-45430800	Genic enhancers	Osteobl	bone
24	chr6:45429000-45440600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:45429200-45430800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:45429200-45431200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:45429200-45432800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:45429400-45431000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:45429400-45432200	Strong transcription	HSMM	muscle
30	chr6:45429400-45438000	Weak transcription	NH-A	brain
31	chr6:45429400-45445400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:45429600-45430400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:45429600-45430400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:45429600-45430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:45429600-45432200	Weak transcription	HSMMtube	muscle
36	chr6:45429600-45437800	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr6:45429600-45444800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:45429600-45444800	Weak transcription	NHEK	skin
39	chr6:45429800-45432400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:45429800-45445000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:45429800-45445400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:45430000-45430400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:45430000-45430800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:45430000-45431600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr6:45430000-45444600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr6:45430200-45430400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr6:45430200-45432200	Weak transcription	Fetal Lung	lung
48	chr6:45430200-45444600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:45430200-45445400	Weak transcription	Primary T cells from cord blood	blood
50	chr6:45430200-45445800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links