Variant report

Variant	rs12621416
Chromosome Location	chr2:54598008-54598009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11125531	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11690242	0.87[CHB][hapmap]
rs13385514	0.94[CEU][hapmap];0.96[CHB][hapmap];0.84[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1405834	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs72919333	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3444221	chr2:54594048-54598146	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54587600-54606200	Weak transcription	Fetal Kidney	kidney
2	chr2:54594600-54598400	Weak transcription	Pancreas	Pancrea
3	chr2:54596800-54600200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:54597000-54599000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:54597200-54601400	Enhancers	Adipose Nuclei	Adipose
6	chr2:54597400-54598600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:54597600-54598200	Enhancers	Fetal Lung	lung
8	chr2:54597600-54598600	Enhancers	NHLF	lung
9	chr2:54597600-54599000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:54597600-54599200	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr2:54597600-54599200	Enhancers	Stomach Smooth Muscle	stomach
12	chr2:54597600-54599800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:54597600-54600000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:54597800-54598200	Enhancers	HSMM	muscle
15	chr2:54597800-54598400	Enhancers	HUVEC	blood vessel
16	chr2:54597800-54598600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:54597800-54598600	Enhancers	Aorta	Aorta
18	chr2:54597800-54598600	Enhancers	Hela-S3	cervix
19	chr2:54597800-54598600	Flanking Active TSS	HSMMtube	muscle
20	chr2:54597800-54598800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:54597800-54599000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:54597800-54599000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:54597800-54599000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:54597800-54599000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:54597800-54599000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:54597800-54599000	Enhancers	Esophagus	oesophagus
27	chr2:54597800-54599000	Enhancers	Ovary	ovary
28	chr2:54597800-54599000	Enhancers	NHDF-Ad	bronchial
29	chr2:54597800-54599200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:54597800-54599200	Enhancers	Brain Anterior Caudate	brain
31	chr2:54597800-54599200	Enhancers	Lung	lung
32	chr2:54597800-54599200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:54597800-54599200	Enhancers	Osteobl	bone
34	chr2:54597800-54599600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:54597800-54600600	Enhancers	Fetal Muscle Trunk	muscle
36	chr2:54597800-54600600	Enhancers	Placenta	Placenta
37	chr2:54597800-54600800	Enhancers	Right Atrium	heart
38	chr2:54597800-54601000	Enhancers	Fetal Muscle Leg	muscle
39	chr2:54597800-54601200	Enhancers	Right Ventricle	heart
40	chr2:54597800-54601400	Enhancers	Left Ventricle	heart
41	chr2:54598000-54599000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr2:54598000-54599000	Enhancers	Fetal Stomach	stomach
43	chr2:54598000-54599800	Bivalent Enhancer	HepG2	liver
44	chr2:54598000-54600000	Enhancers	Fetal Heart	heart

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