Variant report

Variant	rs12648437
Chromosome Location	chr4:76888235-76888236
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	chr4:76879502..76881277-chr4:76887911..76890255,2	K562	blood:
2	chr4:76886922..76890200-chr4:76895899..76900311,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198301	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10337	0.95[ASN][1000 genomes]
rs11726292	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11735706	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12648687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651276	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17001237	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17001273	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271527	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276885	0.82[ASN][1000 genomes]
rs2292534	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28651740	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2869460	0.95[ASN][1000 genomes]
rs3733239	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796482	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796483	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626230	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57946262	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61281201	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61487959	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66932304	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67906710	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68181445	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838162	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6840076	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6841376	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6849878	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7154	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72607852	0.94[ASN][1000 genomes]
rs7654068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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
rs12648437	NUP54	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76862000-76896600	Weak transcription	Stomach Mucosa	stomach
2	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:76867800-76888800	Strong transcription	Liver	Liver
5	chr4:76867800-76900000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
7	chr4:76868000-76899800	Strong transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:76868000-76903000	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:76868000-76903000	Strong transcription	Stomach Smooth Muscle	stomach
10	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
16	chr4:76869200-76900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:76870800-76897600	Strong transcription	Brain Germinal Matrix	brain
18	chr4:76872200-76902800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:76876800-76895200	Strong transcription	Fetal Kidney	kidney
20	chr4:76880600-76893400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:76882400-76898200	Weak transcription	Aorta	Aorta
22	chr4:76883800-76899800	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr4:76883800-76903000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr4:76884000-76902800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:76884200-76899600	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr4:76884200-76899800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:76884200-76902800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:76884200-76903800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr4:76884400-76893000	Strong transcription	Brain Anterior Caudate	brain
30	chr4:76884400-76897400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:76884600-76889400	Strong transcription	Ovary	ovary
32	chr4:76884600-76889800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:76884600-76893400	Strong transcription	HSMMtube	muscle
34	chr4:76884600-76895600	Strong transcription	Fetal Brain Female	brain
35	chr4:76884600-76895800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr4:76884600-76896000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:76884600-76897400	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr4:76884600-76899800	Strong transcription	NH-A	brain
39	chr4:76884600-76899800	Strong transcription	Osteobl	bone
40	chr4:76884600-76902800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:76884600-76902800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:76884600-76902800	Strong transcription	Adipose Nuclei	Adipose
43	chr4:76884600-76903400	Strong transcription	HMEC	breast
44	chr4:76884600-76903400	Strong transcription	HSMM	muscle
45	chr4:76884600-76903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:76884600-76903600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:76884600-76903800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:76884800-76892400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:76884800-76893600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:76884800-76893600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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