Variant report

Variant	rs62260777
Chromosome Location	chr3:105221860-105221861
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16851098	0.83[ASN][1000 genomes]
rs16851279	0.89[AMR][1000 genomes]
rs2062433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291377	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772555	0.89[AMR][1000 genomes]
rs3910551	0.91[ASN][1000 genomes]
rs41380949	0.89[ASN][1000 genomes]
rs56341088	0.86[ASN][1000 genomes]
rs62262966	0.89[AMR][1000 genomes]
rs62262967	0.87[AMR][1000 genomes]
rs62262968	0.87[AMR][1000 genomes]
rs7624892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	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
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105210000-105223000	Weak transcription	Gastric	stomach
2	chr3:105210200-105222000	Weak transcription	NH-A	brain
3	chr3:105210200-105223800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:105210200-105229000	Weak transcription	HSMM	muscle
5	chr3:105210200-105243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:105210600-105223200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:105210800-105222400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:105215600-105223800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:105215800-105223000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:105215800-105223200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:105218200-105222000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr3:105218600-105222400	Enhancers	Brain Angular Gyrus	brain
13	chr3:105219000-105222000	Weak transcription	Fetal Kidney	kidney
14	chr3:105219600-105222000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:105219600-105224000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:105220000-105222600	Weak transcription	Pancreas	Pancrea
17	chr3:105220000-105223000	Enhancers	Osteobl	bone
18	chr3:105220200-105222600	Enhancers	Brain Substantia Nigra	brain
19	chr3:105220200-105223200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:105220200-105223400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:105220200-105223400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:105220600-105222000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:105221000-105222800	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr3:105221200-105222000	Enhancers	Aorta	Aorta
25	chr3:105221200-105222000	Flanking Active TSS	HepG2	liver
26	chr3:105221200-105222600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:105221200-105222800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:105221200-105222800	Enhancers	Brain Anterior Caudate	brain
29	chr3:105221200-105222800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:105221200-105224000	Enhancers	Brain Hippocampus Middle	brain
31	chr3:105221200-105224400	Enhancers	Brain Cingulate Gyrus	brain
32	chr3:105221400-105222000	Flanking Active TSS	Liver	Liver
33	chr3:105221400-105222000	Flanking Active TSS	A549	lung
34	chr3:105221400-105222400	Enhancers	Stomach Mucosa	stomach
35	chr3:105221400-105222600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:105221600-105223000	Weak transcription	Lung	lung
38	chr3:105221600-105223800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:105221600-105229800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:105221600-105231800	Weak transcription	NHLF	lung
41	chr3:105221800-105227600	Weak transcription	Muscle Satellite Cultured Cells	--

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