Variant report

Variant	rs4233949
Chromosome Location	chr2:54659707-54659708
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12713257	0.83[ASN][1000 genomes]
rs13392262	0.83[ASN][1000 genomes]
rs3951717	0.83[ASN][1000 genomes]
rs4315567	0.89[ASN][1000 genomes]
rs4588223	0.83[ASN][1000 genomes]
rs4671213	0.83[ASN][1000 genomes]
rs6545403	0.83[ASN][1000 genomes]
rs6710292	0.83[ASN][1000 genomes]
rs6734097	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6752877	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6760027	0.83[ASN][1000 genomes]
rs7565489	0.83[ASN][1000 genomes]
rs7592359	0.83[ASN][1000 genomes]
rs7592641	0.83[ASN][1000 genomes]
rs7607093	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[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	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bone mineral density	22504420	GWAS catalog

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54654000-54663200	Enhancers	Fetal Muscle Leg	muscle
2	chr2:54654000-54664200	Enhancers	Adipose Nuclei	Adipose
3	chr2:54654200-54660200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr2:54654400-54660600	Enhancers	Fetal Brain Male	brain
5	chr2:54654800-54660600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:54655200-54659800	Enhancers	Stomach Smooth Muscle	stomach
7	chr2:54655200-54660400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:54656000-54660200	Enhancers	Fetal Heart	heart
9	chr2:54656200-54660200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr2:54656600-54660200	Enhancers	Primary hematopoietic stem cells	blood
11	chr2:54656800-54660000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:54656800-54660200	Enhancers	Right Atrium	heart
13	chr2:54656800-54663200	Enhancers	Fetal Lung	lung
14	chr2:54656800-54665200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:54657200-54659800	Enhancers	Brain Substantia Nigra	brain
16	chr2:54657200-54660200	Enhancers	Brain Anterior Caudate	brain
17	chr2:54657200-54660200	Enhancers	Psoas Muscle	Psoas
18	chr2:54657400-54660200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:54657800-54660400	Weak transcription	HSMMtube	muscle
20	chr2:54658200-54660800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr2:54658400-54660200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:54658400-54662200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:54658400-54665400	Weak transcription	Pancreas	Pancrea
24	chr2:54658600-54659800	Weak transcription	Lung	lung
25	chr2:54658600-54660400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr2:54658600-54664000	Weak transcription	Spleen	Spleen
27	chr2:54658800-54660000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:54658800-54660200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:54659000-54659800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr2:54659000-54659800	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr2:54659000-54660000	Enhancers	Colon Smooth Muscle	Colon
32	chr2:54659200-54659800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:54659200-54660000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:54659200-54660000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:54659200-54660000	Enhancers	Fetal Kidney	kidney
36	chr2:54659200-54660200	Enhancers	Brain Angular Gyrus	brain
37	chr2:54659200-54660200	Enhancers	Left Ventricle	heart
38	chr2:54659200-54660600	Enhancers	Brain Hippocampus Middle	brain
39	chr2:54659200-54660800	Enhancers	Fetal Stomach	stomach
40	chr2:54659400-54659800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:54659400-54659800	Enhancers	HUVEC	blood vessel
42	chr2:54659400-54660000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr2:54659600-54660200	Enhancers	Fetal Muscle Trunk	muscle
44	chr2:54659600-54660200	Enhancers	Right Ventricle	heart
45	chr2:54659600-54660600	Enhancers	Ovary	ovary

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