Variant report

Variant	rs12490553
Chromosome Location	chr3:105210206-105210207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs6769329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620022	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833451	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9857705	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9857961	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][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:38 , 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	chr3:105209000-105210400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr3:105209000-105210600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
7	chr3:105209200-105210400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
8	chr3:105209200-105210600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
9	chr3:105209200-105210800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:105209400-105210400	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr3:105209400-105210400	ZNF genes & repeats	Liver	Liver
12	chr3:105209400-105210600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
13	chr3:105209400-105210600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
14	chr3:105209600-105210400	ZNF genes & repeats	Brain Hippocampus Middle	brain
15	chr3:105209600-105211000	Weak transcription	Fetal Heart	heart
16	chr3:105209800-105210400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr3:105209800-105210400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
18	chr3:105209800-105210800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:105209800-105211000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:105210000-105210400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
21	chr3:105210000-105212800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:105210000-105213200	Weak transcription	Brain Anterior Caudate	brain
23	chr3:105210000-105223000	Weak transcription	Gastric	stomach
24	chr3:105210200-105210600	Weak transcription	Lung	lung
25	chr3:105210200-105210800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:105210200-105211800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:105210200-105213400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:105210200-105213600	Weak transcription	Aorta	Aorta
29	chr3:105210200-105215600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:105210200-105218400	Weak transcription	A549	lung
31	chr3:105210200-105218800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:105210200-105220600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:105210200-105220800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:105210200-105221200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:105210200-105222000	Weak transcription	NH-A	brain
36	chr3:105210200-105223800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:105210200-105229000	Weak transcription	HSMM	muscle
38	chr3:105210200-105243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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