Variant report

Variant	rs2920839
Chromosome Location	chr2:55283082-55283083
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55282373..55283908-chr2:55365419..55368090,2	K562	blood:
2	chr2:55280650..55283253-chr2:55298459..55300307,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10179594	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205017	0.90[EUR][1000 genomes]
rs12989576	0.93[EUR][1000 genomes]
rs13002841	0.90[EUR][1000 genomes]
rs13023202	0.91[EUR][1000 genomes]
rs2580763	0.87[EUR][1000 genomes]
rs2580766	0.91[EUR][1000 genomes]
rs2588520	0.91[EUR][1000 genomes]
rs2919125	0.91[EUR][1000 genomes]
rs2920861	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920863	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2920881	0.81[ASN][1000 genomes]
rs2920883	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920884	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920889	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920890	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920897	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968789	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968792	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968823	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968824	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968826	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968829	0.84[ASN][1000 genomes]
rs2968831	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972065	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972066	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972067	0.81[ASN][1000 genomes]
rs2972069	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972073	0.81[ASN][1000 genomes]
rs2972076	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3099068	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72912591	0.92[AFR][1000 genomes]
rs7559248	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2920839	RTN4	cis	Thyroid	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55278200-55288800	Weak transcription	Lung	lung
2	chr2:55278800-55283200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:55278800-55283200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:55278800-55288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:55278800-55290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:55279000-55283200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:55279000-55287000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:55279000-55290600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:55279400-55283200	Weak transcription	Osteobl	bone
10	chr2:55279400-55283400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:55279400-55283400	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:55279400-55287600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:55279600-55283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:55279800-55283200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:55279800-55283200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:55279800-55283200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:55279800-55283200	Weak transcription	NHDF-Ad	bronchial
18	chr2:55279800-55284200	Weak transcription	Fetal Intestine Small	intestine
19	chr2:55279800-55284400	Weak transcription	Fetal Heart	heart
20	chr2:55279800-55287400	Weak transcription	HSMM	muscle
21	chr2:55280000-55283200	Weak transcription	HMEC	breast
22	chr2:55280000-55289000	Weak transcription	HepG2	liver
23	chr2:55280200-55283200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:55280200-55283200	Weak transcription	A549	lung
25	chr2:55280200-55287200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:55280200-55288200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr2:55281800-55287600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:55282000-55283200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr2:55282000-55283200	Weak transcription	K562	blood
30	chr2:55282400-55283400	Weak transcription	GM12878-XiMat	blood
31	chr2:55282800-55283400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:55283000-55283400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:55283000-55283400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:55283000-55283600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:55283000-55284200	Enhancers	Primary B cells from cord blood	blood

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