Variant report

Variant	rs61281201
Chromosome Location	chr4:76868576-76868577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76866002..76869034-chr4:76870161..76872901,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NAAA-1	chr4:76868484-76868819	ucscGeneNc_uc010iiy_1

Variant related genes	Relation type
ENSG00000268788	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10337	0.92[ASN][1000 genomes]
rs11726292	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735706	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12648437	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12648687	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12651276	0.90[ASN][1000 genomes]
rs17001237	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17001273	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271527	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292534	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28651740	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2869460	0.92[ASN][1000 genomes]
rs3733239	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796482	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796483	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4626230	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57946262	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61487959	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66932304	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67906710	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68181445	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6838162	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6840076	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6841376	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6849878	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7154	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72607852	0.90[ASN][1000 genomes]
rs7654068	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	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
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61281201	NUP54	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76862000-76871600	Weak transcription	Fetal Kidney	kidney
2	chr4:76862000-76875600	Weak transcription	Fetal Heart	heart
3	chr4:76862000-76896600	Weak transcription	Stomach Mucosa	stomach
4	chr4:76862200-76871000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:76862200-76871000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:76862200-76875200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:76862200-76876400	Weak transcription	Gastric	stomach
8	chr4:76862200-76876600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:76862200-76886600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:76862400-76868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:76862400-76873400	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:76862400-76875400	Weak transcription	Spleen	Spleen
13	chr4:76862400-76876600	Weak transcription	Aorta	Aorta
14	chr4:76862400-76876600	Weak transcription	Small Intestine	intestine
15	chr4:76862600-76869200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:76862600-76869800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:76862600-76870600	Weak transcription	Brain Substantia Nigra	brain
18	chr4:76862600-76870800	Weak transcription	Brain Germinal Matrix	brain
19	chr4:76862600-76871000	Weak transcription	Brain Angular Gyrus	brain
20	chr4:76862600-76871000	Weak transcription	Brain Anterior Caudate	brain
21	chr4:76862600-76871400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:76862600-76871400	Weak transcription	Right Ventricle	heart
23	chr4:76862600-76871600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:76862600-76872000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:76862600-76872000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:76862600-76873200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:76862600-76873400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:76862600-76873400	Weak transcription	NHLF	lung
29	chr4:76862600-76873600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr4:76862600-76874400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:76862600-76876000	Weak transcription	Psoas Muscle	Psoas
32	chr4:76862600-76876400	Weak transcription	Esophagus	oesophagus
33	chr4:76862600-76876400	Weak transcription	Fetal Brain Male	brain
34	chr4:76862600-76876400	Weak transcription	Pancreas	Pancrea
35	chr4:76862600-76876800	Weak transcription	Hela-S3	cervix
36	chr4:76862800-76869800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:76863600-76870000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:76863800-76884600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:76864600-76884800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:76864800-76875200	Strong transcription	HSMM	muscle
42	chr4:76864800-76883800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:76864800-76884400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:76864800-76884600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:76866200-76883000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:76866400-76886800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:76866600-76883000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:76867200-76869000	Strong transcription	Fetal Intestine Small	intestine
50	chr4:76867400-76869400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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