Variant report

Variant	rs55965048
Chromosome Location	chr1:225884653-225884654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10915857	0.82[AFR][1000 genomes]
rs17504298	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17569722	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1857009	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653424	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653425	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653426	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653647	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653648	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653651	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56260304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426082	0.89[AFR][1000 genomes]
rs6694288	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753075	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7365361	0.80[AFR][1000 genomes]
rs7365591	0.80[AFR][1000 genomes]
rs7366333	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7521926	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7552440	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225865600-225888000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:225875200-225898600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:225878600-225885400	Enhancers	Left Ventricle	heart
4	chr1:225879400-225887000	Weak transcription	NHLF	lung
5	chr1:225880800-225887800	Weak transcription	Spleen	Spleen
6	chr1:225881000-225887200	Weak transcription	Right Ventricle	heart
7	chr1:225881800-225885600	Enhancers	Fetal Stomach	stomach
8	chr1:225882000-225885400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:225882000-225885600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:225882200-225887000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:225882200-225889600	Enhancers	Fetal Muscle Leg	muscle
12	chr1:225882400-225887000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:225882400-225887000	Weak transcription	Hela-S3	cervix
14	chr1:225882400-225887200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:225882400-225887200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:225882400-225908000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:225882800-225887000	Weak transcription	Stomach Mucosa	stomach
18	chr1:225883000-225885200	Weak transcription	Lung	lung
19	chr1:225883000-225887000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:225883000-225887000	Weak transcription	HUVEC	blood vessel
21	chr1:225883000-225887200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:225883400-225885400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:225883400-225885600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:225883400-225887200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:225883600-225885600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:225883600-225885600	Enhancers	Fetal Lung	lung
27	chr1:225883600-225887000	Weak transcription	HMEC	breast
28	chr1:225883600-225887000	Weak transcription	NHEK	skin
29	chr1:225883600-225887200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:225883800-225885200	Enhancers	HSMMtube	muscle
31	chr1:225883800-225885800	Enhancers	Fetal Muscle Trunk	muscle
32	chr1:225884000-225885000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:225884000-225885000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:225884000-225885200	Weak transcription	Right Atrium	heart
35	chr1:225884000-225885400	Enhancers	Placenta	Placenta
36	chr1:225884000-225887000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:225884000-225887000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:225884000-225887000	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:225884000-225887000	Weak transcription	Fetal Heart	heart
40	chr1:225884000-225887000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:225884000-225887000	Weak transcription	NHDF-Ad	bronchial
42	chr1:225884000-225887200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:225884000-225887800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:225884200-225885200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:225884200-225885200	Weak transcription	A549	lung
46	chr1:225884200-225886600	Weak transcription	Aorta	Aorta
47	chr1:225884200-225886800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:225884200-225887200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:225884200-225887200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:225884400-225884800	Weak transcription	Ovary	ovary

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