Variant report

Variant	rs58999138
Chromosome Location	chr3:105209490-105209491
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs16851323	1.00[AMR][1000 genomes]
rs35248527	1.00[AMR][1000 genomes]
rs55820772	1.00[AFR][1000 genomes]
rs55866944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55924889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56236143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58474331	1.00[AMR][1000 genomes]
rs6437596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6437597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6437598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6765665	1.00[AMR][1000 genomes]
rs6793359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73854306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73854308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73854309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73854310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7618851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7632648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7632662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7640268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7643467	1.00[AFR][1000 genomes]
rs7646694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105193000-105215400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:105193200-105213600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:105201200-105214600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:105205400-105213800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:105207600-105209600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:105207800-105209600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:105207800-105209600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:105208800-105209600	Enhancers	Fetal Heart	heart
9	chr3:105208800-105209600	Weak transcription	Lung	lung
10	chr3:105208800-105210200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:105209000-105210200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:105209000-105210200	ZNF genes & repeats	A549	lung
13	chr3:105209000-105210400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr3:105209000-105210600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
15	chr3:105209200-105210000	ZNF genes & repeats	Brain Anterior Caudate	brain
16	chr3:105209200-105210200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
17	chr3:105209200-105210400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
18	chr3:105209200-105210600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr3:105209200-105210800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:105209400-105209800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:105209400-105209800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr3:105209400-105210000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:105209400-105210000	ZNF genes & repeats	Dnd41	blood
24	chr3:105209400-105210200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:105209400-105210200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:105209400-105210200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:105209400-105210200	ZNF genes & repeats	Primary B cells from cord blood	blood
28	chr3:105209400-105210200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:105209400-105210200	ZNF genes & repeats	GM12878-XiMat	blood
30	chr3:105209400-105210200	ZNF genes & repeats	HSMM	muscle
31	chr3:105209400-105210200	ZNF genes & repeats	NH-A	brain
32	chr3:105209400-105210400	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr3:105209400-105210400	ZNF genes & repeats	Liver	Liver
34	chr3:105209400-105210600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
35	chr3:105209400-105210600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain

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