Variant report

Variant	rs59050354
Chromosome Location	chr4:77035018-77035019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:77031133..77035310-chr4:77057270..77059295,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10033843	0.81[ASN][1000 genomes]
rs11097237	0.81[ASN][1000 genomes]
rs1127705	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499900	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510869	0.80[ASN][1000 genomes]
rs12641529	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12645639	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646166	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12648162	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12648709	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13130116	0.81[ASN][1000 genomes]
rs13141802	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17001409	0.80[ASN][1000 genomes]
rs17001416	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053486	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28590424	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34022163	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34978911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36081173	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4859423	0.81[ASN][1000 genomes]
rs4859424	0.82[ASN][1000 genomes]
rs4859425	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859617	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859618	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61153596	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66599877	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824367	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72870920	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7689378	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894244	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59050354	NUP54	cis	Esophagus Muscularis	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77027200-77035400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:77027600-77037400	Weak transcription	Brain Substantia Nigra	brain
3	chr4:77027800-77036400	Weak transcription	Brain Angular Gyrus	brain
4	chr4:77027800-77038400	Weak transcription	Fetal Brain Male	brain
5	chr4:77028000-77037600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:77028000-77068600	Weak transcription	Gastric	stomach
7	chr4:77030000-77037400	Weak transcription	NHDF-Ad	bronchial
8	chr4:77030600-77036400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:77030600-77038400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:77031200-77037800	Weak transcription	NHLF	lung
11	chr4:77031600-77039200	Weak transcription	Fetal Intestine Small	intestine
12	chr4:77031800-77036200	Weak transcription	Primary B cells from cord blood	blood
13	chr4:77031800-77036200	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:77032000-77036200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:77032000-77036400	Weak transcription	Aorta	Aorta
16	chr4:77032000-77037600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:77032200-77035200	Strong transcription	Left Ventricle	heart
18	chr4:77032200-77049200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:77032400-77037400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:77032400-77037600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:77032600-77067600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:77032800-77036800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:77032800-77039600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:77033000-77037600	Weak transcription	NHEK	skin
25	chr4:77033000-77037800	Weak transcription	Colonic Mucosa	Colon
26	chr4:77033000-77044800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:77033000-77046800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr4:77033000-77046800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:77033000-77052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:77033200-77035200	Strong transcription	Fetal Stomach	stomach
31	chr4:77033200-77036200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:77033200-77038200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:77033200-77038400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr4:77033200-77038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:77033200-77044400	Weak transcription	Spleen	Spleen
36	chr4:77033200-77045200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:77033200-77045600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr4:77033200-77046200	Strong transcription	Liver	Liver
39	chr4:77033200-77046600	Strong transcription	Fetal Lung	lung
40	chr4:77033200-77058200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:77033200-77066000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:77033200-77068400	Weak transcription	Small Intestine	intestine
43	chr4:77033400-77035200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:77033400-77035200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr4:77033400-77035400	Strong transcription	Thymus	Thymus
46	chr4:77033400-77036800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:77033400-77038400	Strong transcription	Primary T cells from cord blood	blood
48	chr4:77033400-77039400	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr4:77033400-77039800	Strong transcription	HSMM	muscle
50	chr4:77033400-77040600	Weak transcription	Lung	lung

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