Variant report

Variant	rs9864062
Chromosome Location	chr3:105192235-105192236
allele	A/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:15)

rs_ID	r²[population]
rs1017913	0.85[JPT][hapmap]
rs1017914	0.85[JPT][hapmap]
rs1036581	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13100997	0.82[EUR][1000 genomes]
rs1994317	0.85[JPT][hapmap]
rs2033802	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2053307	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2252459	0.85[JPT][hapmap]
rs4894924	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6790159	0.81[EUR][1000 genomes]
rs7428824	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7641185	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9827147	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9827196	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9870921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	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

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105179600-105192400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:105185200-105193000	Weak transcription	Aorta	Aorta
3	chr3:105185800-105192400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:105186200-105194000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:105189800-105192600	Enhancers	Brain Substantia Nigra	brain
6	chr3:105189800-105192800	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:105190200-105192400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:105190400-105192400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:105190400-105192400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:105190600-105194000	Enhancers	Brain Anterior Caudate	brain
11	chr3:105191200-105193000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:105191200-105193200	Enhancers	NH-A	brain
13	chr3:105191200-105193200	Enhancers	Osteobl	bone
14	chr3:105191200-105194000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:105191400-105192400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:105191400-105192800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:105191400-105193000	Enhancers	HSMMtube	muscle
18	chr3:105191400-105193200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:105191400-105193200	Enhancers	HSMM	muscle
20	chr3:105191400-105200600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:105191600-105192800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:105192000-105192800	Enhancers	Brain Hippocampus Middle	brain
23	chr3:105192000-105193000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:105192200-105192600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:105192200-105192600	Enhancers	NHDF-Ad	bronchial
26	chr3:105192200-105192800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:105192200-105192800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:105192200-105192800	Enhancers	A549	lung
29	chr3:105192200-105192800	Enhancers	NHEK	skin
30	chr3:105192200-105193000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:105192200-105193000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:105192200-105193000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:105192200-105193000	Enhancers	Brain Angular Gyrus	brain
34	chr3:105192200-105193200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:105192200-105193200	Enhancers	GM12878-XiMat	blood
36	chr3:105192200-105193200	Enhancers	HMEC	breast
37	chr3:105192200-105193400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr3:105192200-105194000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:105192200-105194000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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