Variant report

Variant	rs28590424
Chromosome Location	chr4:77047219-77047220
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1127705	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12499900	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641529	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645639	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646166	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12648162	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12648709	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141802	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17001416	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2053486	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34022163	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34978911	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35713908	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36081173	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4859424	0.80[ASN][1000 genomes]
rs4859425	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859617	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859618	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59050354	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61153596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66599877	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824367	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72870920	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673428	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7689378	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs894244	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv470047	chr4:77033590-77096777	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv594693	chr4:77033590-77101068	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv275315	chr4:77040424-77056493	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1008318	chr4:77042356-77095658	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv537144	chr4:77042356-77095658	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	nsv1000539	chr4:77042356-77105492	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28590424	NUP54	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77028000-77068600	Weak transcription	Gastric	stomach
2	chr4:77032200-77049200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:77032600-77067600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:77033000-77052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:77033200-77058200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:77033200-77066000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:77033200-77068400	Weak transcription	Small Intestine	intestine
8	chr4:77033400-77047800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:77033400-77048200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr4:77033400-77052000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:77033400-77052200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:77033400-77065600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:77033400-77066000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:77033400-77066600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr4:77033600-77047600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr4:77033600-77065600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr4:77033800-77066200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:77034000-77054000	Strong transcription	Dnd41	blood
19	chr4:77034000-77066000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:77034400-77067200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:77035000-77068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:77035200-77062000	Weak transcription	Esophagus	oesophagus
23	chr4:77035200-77068600	Weak transcription	Pancreas	Pancrea
24	chr4:77035400-77066000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:77035600-77068400	Weak transcription	Right Ventricle	heart
26	chr4:77036400-77054600	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr4:77038200-77062000	Weak transcription	Aorta	Aorta
28	chr4:77038800-77051600	Weak transcription	Hela-S3	cervix
29	chr4:77039000-77050400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:77039000-77061800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:77039000-77068200	Weak transcription	Psoas Muscle	Psoas
32	chr4:77039000-77068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:77039400-77056000	Weak transcription	Stomach Mucosa	stomach
34	chr4:77039400-77056600	Weak transcription	Brain Substantia Nigra	brain
35	chr4:77039400-77056600	Weak transcription	Fetal Brain Male	brain
36	chr4:77039400-77056800	Weak transcription	NHLF	lung
37	chr4:77039600-77057400	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:77039800-77056600	Weak transcription	Colonic Mucosa	Colon
39	chr4:77040400-77049000	Weak transcription	Fetal Brain Female	brain
40	chr4:77040800-77056800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr4:77040800-77063200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:77041000-77049000	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:77041000-77049200	Weak transcription	Fetal Stomach	stomach
44	chr4:77041000-77056800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:77041600-77049200	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:77041600-77050600	Weak transcription	Thymus	Thymus
47	chr4:77041800-77057600	Weak transcription	Ovary	ovary
48	chr4:77042600-77049000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:77043000-77048000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:77043600-77059400	Weak transcription	Brain Cingulate Gyrus	brain

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