Variant report

Variant	rs58953554
Chromosome Location	chr3:99865246-99865247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs16842137	1.00[AMR][1000 genomes]
rs403858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55721822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55978866	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56186146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56227134	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56678433	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58283662	1.00[AMR][1000 genomes]
rs58869093	1.00[AMR][1000 genomes]
rs59674041	1.00[AMR][1000 genomes]
rs62636639	1.00[AMR][1000 genomes]
rs6441136	1.00[AMR][1000 genomes]
rs6783067	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859916	1.00[AMR][1000 genomes]
rs73859919	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859921	1.00[AMR][1000 genomes]
rs73859924	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859925	0.93[AFR][1000 genomes]
rs73859931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73862419	1.00[AMR][1000 genomes]
rs73862437	1.00[AMR][1000 genomes]
rs73862440	1.00[AMR][1000 genomes]
rs73862445	1.00[AMR][1000 genomes]
rs73862453	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99847000-99868800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:99855400-99868000	Weak transcription	Left Ventricle	heart
4	chr3:99856000-99868000	Weak transcription	Aorta	Aorta
5	chr3:99856000-99877800	Weak transcription	Ovary	ovary
6	chr3:99858600-99865800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:99858600-99868600	Weak transcription	Pancreas	Pancrea
8	chr3:99858600-99877200	Weak transcription	HSMM	muscle
9	chr3:99859200-99870200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:99860200-99874000	Weak transcription	A549	lung
11	chr3:99860800-99868000	Weak transcription	Fetal Stomach	stomach
12	chr3:99860800-99868400	Weak transcription	NHDF-Ad	bronchial
13	chr3:99861000-99870000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:99861600-99870400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:99862000-99868200	Weak transcription	Primary B cells from cord blood	blood
16	chr3:99862200-99874200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:99862800-99870000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:99863200-99866000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:99863200-99866400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:99863400-99872200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:99863400-99873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:99863400-99874000	Weak transcription	NHEK	skin
23	chr3:99863600-99868600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:99863600-99874000	Weak transcription	GM12878-XiMat	blood
25	chr3:99863800-99866400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:99863800-99866600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:99863800-99873000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:99863800-99873600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:99863800-99874000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:99864000-99873400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr3:99864400-99886600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:99864600-99870800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:99864600-99873600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:99864800-99869000	Weak transcription	Fetal Lung	lung
35	chr3:99865000-99866600	Weak transcription	K562	blood
36	chr3:99865000-99873400	Weak transcription	Fetal Intestine Small	intestine
37	chr3:99865000-99894600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links