Variant report

Variant	rs72949902
Chromosome Location	chr1:86849644-86849645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11161796	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11161797	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11801454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11803763	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11804733	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11810074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12079988	1.00[AMR][1000 genomes]
rs12096446	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34372019	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56841249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949810	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949857	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949858	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949875	1.00[AFR][1000 genomes]
rs72949879	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951830	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951845	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1793594	chr1:86833653-86858957	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
2	chr1:86818000-86851600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:86820200-86854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:86820200-86854800	Weak transcription	HSMMtube	muscle
5	chr1:86820400-86860200	Weak transcription	NHEK	skin
6	chr1:86836600-86860800	Weak transcription	Aorta	Aorta
7	chr1:86840600-86859600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:86841000-86851400	Weak transcription	HMEC	breast
9	chr1:86841000-86854400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:86841000-86859800	Weak transcription	HSMM	muscle
11	chr1:86841600-86859800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:86841800-86855000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:86843400-86855000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:86843400-86860800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:86843600-86858600	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:86843600-86859200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:86843600-86860600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:86843600-86860800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:86843800-86854000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:86844600-86853400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:86844800-86855000	Weak transcription	Thymus	Thymus
22	chr1:86844800-86859200	Weak transcription	Brain Germinal Matrix	brain
23	chr1:86844800-86861000	Weak transcription	Fetal Intestine Small	intestine
24	chr1:86845000-86850800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:86845000-86853800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:86845000-86855000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:86845000-86859200	Weak transcription	NH-A	brain
28	chr1:86845000-86859400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:86845000-86860200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:86845000-86860600	Weak transcription	Fetal Thymus	thymus
31	chr1:86845000-86860800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:86845200-86859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:86845800-86851200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:86846600-86860400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:86846800-86853600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:86847400-86849800	Weak transcription	Liver	Liver
37	chr1:86848200-86849800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:86848400-86849800	Enhancers	Primary T cells from cord blood	blood
39	chr1:86848800-86861000	Weak transcription	Primary B cells from cord blood	blood
40	chr1:86849000-86858600	Weak transcription	NHDF-Ad	bronchial
41	chr1:86849200-86849800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:86849200-86849800	Enhancers	Dnd41	blood
43	chr1:86849200-86849800	Genic enhancers	HUVEC	blood vessel
44	chr1:86849200-86853400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:86849200-86853800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:86849200-86854600	Weak transcription	GM12878-XiMat	blood
47	chr1:86849200-86855000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:86849200-86860200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:86849200-86860800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:86849400-86849800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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