Variant report

Variant	rs6690245
Chromosome Location	chr1:56992416-56992417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10157636	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10888977	0.81[JPT][hapmap]
rs11583161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11590570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12081589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12084507	0.93[ASN][1000 genomes]
rs1759752	0.82[JPT][hapmap]
rs4912314	0.95[JPT][hapmap]
rs57966457	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58289463	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60314060	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664330	0.93[ASN][1000 genomes]
rs7512545	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7515808	0.95[JPT][hapmap]
rs7519268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7549894	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7554557	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56967000-57002000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:56977800-56999200	Weak transcription	A549	lung
3	chr1:56978000-56992600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:56979200-56992600	Strong transcription	HepG2	liver
5	chr1:56983400-57000800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:56985000-56993400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:56985000-56993600	Weak transcription	Fetal Brain Female	brain
8	chr1:56986200-56992600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
10	chr1:56987600-56994200	Enhancers	Dnd41	blood
11	chr1:56987800-56993000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr1:56988400-56992800	Enhancers	Right Atrium	heart
13	chr1:56988400-56993800	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:56989400-56993600	Enhancers	Primary B cells from cord blood	blood
15	chr1:56990000-56992600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:56990000-56995200	Genic enhancers	Fetal Muscle Leg	muscle
17	chr1:56990000-57004000	Genic enhancers	Liver	Liver
18	chr1:56990200-56992800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:56990200-56993600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:56990200-56994400	Enhancers	Fetal Thymus	thymus
21	chr1:56990200-56998600	Enhancers	Brain Substantia Nigra	brain
22	chr1:56990400-56993200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:56990400-56996200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:56990600-56992600	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:56990600-56992600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:56990600-56992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:56990600-56992800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:56990600-56992800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
29	chr1:56990600-56994000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:56990600-56995400	Enhancers	Small Intestine	intestine
31	chr1:56990600-56996600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:56990600-56997800	Enhancers	Brain Anterior Caudate	brain
33	chr1:56990800-56993200	Genic enhancers	HSMM	muscle
34	chr1:56990800-56994000	Enhancers	Thymus	Thymus
35	chr1:56990800-56994200	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr1:56990800-56996600	Genic enhancers	NHLF	lung
37	chr1:56990800-56997000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:56990800-56997200	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:56990800-56997400	Enhancers	Brain Hippocampus Middle	brain
40	chr1:56991000-56992600	Enhancers	Brain Angular Gyrus	brain
41	chr1:56991000-56992800	Enhancers	HMEC	breast
42	chr1:56991000-56996200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:56991200-56992600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:56991200-56992800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:56991200-56992800	Enhancers	HSMMtube	muscle
46	chr1:56991200-56993000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:56991200-56993800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:56991200-56993800	Enhancers	Fetal Kidney	kidney
49	chr1:56991200-56994000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:56991200-56994200	Enhancers	Psoas Muscle	Psoas

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