Variant report

Variant	rs2820340
Chromosome Location	chr6:45424498-45424499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45419545..45421577-chr6:45423010..45426161,3	MCF-7	breast:
2	chr6:45415340..45418942-chr6:45422164..45424791,5	K562	blood:
3	chr6:45423983..45426687-chr6:45430740..45433048,2	MCF-7	breast:
4	chr6:45416242..45417772-chr6:45424221..45426161,2	MCF-7	breast:

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];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12197948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12210100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12215249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1317777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[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];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934327	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2252718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2256819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396442	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2677098	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677099	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677100	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677109	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790094	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790095	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2790097	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790099	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790100	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]
rs2790102	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819865	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819866	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2819867	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4711816	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4714854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765724	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7756144	0.87[EUR][1000 genomes]
rs910586	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9472494	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9885645	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[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:54 , 50 per page) page: 1 2

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	chr6:45415600-45424600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:45416400-45430600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:45416400-45440400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:45416600-45430000	Weak transcription	Small Intestine	intestine
7	chr6:45418200-45427400	Weak transcription	Aorta	Aorta
8	chr6:45419200-45456200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:45419400-45429000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:45420000-45425200	Strong transcription	Dnd41	blood
11	chr6:45420800-45425600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:45421200-45428800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:45422000-45425200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:45422000-45425400	Weak transcription	Fetal Thymus	thymus
15	chr6:45422000-45428800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:45422000-45429000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:45422000-45429000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:45422000-45441200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:45422000-45445000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:45422200-45424800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:45422200-45440000	Weak transcription	Brain Angular Gyrus	brain
22	chr6:45422400-45425200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:45422400-45427800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr6:45422400-45428800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr6:45422400-45429000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:45422400-45438200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:45422600-45424800	Weak transcription	HMEC	breast
28	chr6:45422600-45424800	Weak transcription	NHEK	skin
29	chr6:45422600-45425000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:45422600-45428000	Weak transcription	HSMMtube	muscle
31	chr6:45422600-45429200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:45422600-45432400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:45422600-45437200	Weak transcription	NHDF-Ad	bronchial
34	chr6:45422600-45439800	Weak transcription	NHLF	lung
35	chr6:45422800-45428800	Strong transcription	HSMM	muscle
36	chr6:45423000-45425600	Strong transcription	Osteobl	bone
37	chr6:45423000-45428200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:45423000-45454400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:45423200-45425200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:45423400-45425000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:45423400-45426600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:45423400-45428800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:45423400-45434600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:45423600-45424800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:45423600-45429200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:45423800-45429200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:45424000-45425200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:45424000-45425400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:45424200-45424600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:45424200-45425000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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