Variant report

Variant	rs6458443
Chromosome Location	chr6:45408440-45408441
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45345002..45348666-chr6:45406844..45410633,4	K562	blood:
2	chr6:45388663..45390976-chr6:45406985..45408759,2	MCF-7	breast:
3	chr6:45404085..45406503-chr6:45408205..45409935,3	K562	blood:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction
ENSG00000271857	Chromatin interaction
ENSG00000124813	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10214519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12197948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12210100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12215249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1316330	1.00[CHB][hapmap]
rs1317777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13201287	0.80[CEU][hapmap]
rs13208741	1.00[CHB][hapmap];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];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934327	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2252718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2256819	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396442	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2677098	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677099	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677100	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677109	0.90[CEU][hapmap];0.99[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[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];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790094	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790095	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2790097	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790099	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790100	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]
rs2790102	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819865	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819866	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2819867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2820340	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]
rs4711816	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4714854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs765724	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7756144	0.92[EUR][1000 genomes]
rs910586	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9472494	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9885645	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45394400-45413200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:45399400-45423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:45399800-45410600	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr6:45400200-45409600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:45402000-45413200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:45403000-45410600	Enhancers	Fetal Thymus	thymus
7	chr6:45403800-45413200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:45405000-45413000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:45405000-45413200	Weak transcription	Brain Anterior Caudate	brain
10	chr6:45405200-45417200	Weak transcription	Spleen	Spleen
11	chr6:45405400-45413400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:45405600-45411600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:45405600-45412200	Weak transcription	Primary B cells from cord blood	blood
14	chr6:45405600-45412400	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:45405600-45413200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:45405600-45413200	Weak transcription	Brain Substantia Nigra	brain
17	chr6:45405600-45413400	Weak transcription	Brain Angular Gyrus	brain
18	chr6:45405600-45413800	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:45405600-45417400	Genic enhancers	Dnd41	blood
20	chr6:45405800-45409400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:45406400-45412000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:45406600-45412200	Weak transcription	Fetal Intestine Small	intestine
23	chr6:45407000-45413200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:45407000-45413400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:45407200-45413000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:45407200-45413000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:45407200-45413200	Weak transcription	Fetal Kidney	kidney
28	chr6:45407200-45413200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:45407200-45413800	Weak transcription	Aorta	Aorta
30	chr6:45407200-45418200	Weak transcription	Gastric	stomach
31	chr6:45407200-45462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:45407400-45408800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:45407400-45409600	Weak transcription	HSMMtube	muscle
34	chr6:45407400-45411400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:45407400-45411400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:45407400-45411800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:45407400-45411800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr6:45407400-45412000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:45407400-45413000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:45407400-45413600	Weak transcription	Primary T cells from cord blood	blood
41	chr6:45407600-45409000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr6:45407600-45409400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:45407600-45409600	Weak transcription	Fetal Lung	lung
44	chr6:45407600-45412000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:45407600-45412000	Weak transcription	Hela-S3	cervix
46	chr6:45407800-45408800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:45407800-45408800	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr6:45407800-45409000	Strong transcription	NH-A	brain
49	chr6:45407800-45409000	Weak transcription	NHDF-Ad	bronchial
50	chr6:45407800-45409000	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links