Variant report

Variant	rs11904342
Chromosome Location	chr2:54600556-54600557
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11895729	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13000039	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13009959	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13023335	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13184	1.00[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1385275	0.84[CHB][hapmap]
rs1682139	0.84[CHB][hapmap]
rs1727530	0.84[CHB][hapmap]
rs34474573	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35123043	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35421399	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4077591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62138163	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739530	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6761635	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11904342	RTN4	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54587600-54606200	Weak transcription	Fetal Kidney	kidney
2	chr2:54597200-54601400	Enhancers	Adipose Nuclei	Adipose
3	chr2:54597800-54600600	Enhancers	Fetal Muscle Trunk	muscle
4	chr2:54597800-54600600	Enhancers	Placenta	Placenta
5	chr2:54597800-54600800	Enhancers	Right Atrium	heart
6	chr2:54597800-54601000	Enhancers	Fetal Muscle Leg	muscle
7	chr2:54597800-54601200	Enhancers	Right Ventricle	heart
8	chr2:54597800-54601400	Enhancers	Left Ventricle	heart
9	chr2:54598400-54601000	Enhancers	Psoas Muscle	Psoas
10	chr2:54598400-54602000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:54598800-54611000	Weak transcription	Brain Substantia Nigra	brain
12	chr2:54599000-54601200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:54599000-54601800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:54599000-54601800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:54599000-54605000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:54599000-54607800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:54599000-54611800	Weak transcription	Ovary	ovary
18	chr2:54599000-54614800	Weak transcription	Pancreas	Pancrea
19	chr2:54599200-54601200	Weak transcription	Fetal Lung	lung
20	chr2:54599200-54611200	Weak transcription	Brain Angular Gyrus	brain
21	chr2:54599600-54601000	Enhancers	Lung	lung
22	chr2:54599600-54601400	Enhancers	HSMMtube	muscle
23	chr2:54599600-54607600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:54599800-54600800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:54600000-54601400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr2:54600000-54605000	Weak transcription	Fetal Heart	heart
27	chr2:54600200-54600600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:54600400-54600600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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