Variant report

Variant	rs28588114
Chromosome Location	chr4:76858000-76858001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr4:76857702-76858016	GM12878	blood:	n/a	chr4:76857882-76857892 chr4:76857860-76857871 chr4:76857859-76857872

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76852145..76854131-chr4:76857580..76859399,2	MCF-7	breast:
2	chr4:76857067..76859381-chr4:76860422..76862398,2	K562	blood:

Variant related genes	Relation type
NAAA	TF binding region
ENSG00000138744	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10009947	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10021434	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10031733	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10518143	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12374321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374370	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13105416	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13112512	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13118503	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13129896	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17001247	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1857821	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242470	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271528	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276886	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28375800	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28422144	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28451731	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28532601	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28535831	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28595360	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647886	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869462	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34630680	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34740469	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733238	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3796484	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4241577	0.83[AMR][1000 genomes]
rs4859567	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4859568	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859569	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4859570	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859571	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859572	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859577	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859578	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859580	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs55876513	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66498356	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6847815	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs884004	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs28588114	NAAA	cis	Esophagus Mucosa	GTEx
rs28588114	NAAA	cis	Muscle Skeletal	GTEx
rs28588114	NAAA	cis	Adipose Subcutaneous	GTEx
rs28588114	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs28588114	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs28588114	NAAA	cis	Artery Aorta	GTEx
rs28588114	NAAA	cis	Whole Blood	GTEx
rs28588114	NAAA	cis	Esophagus Muscularis	GTEx
rs28588114	ASAHL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76832600-76859000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr4:76833800-76860800	Weak transcription	Fetal Heart	heart
3	chr4:76835000-76859400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:76835000-76859600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:76835200-76859800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:76837000-76860200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr4:76837200-76860800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:76837200-76860800	Weak transcription	HSMM	muscle
9	chr4:76837600-76858400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:76837600-76859200	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:76837600-76860800	Weak transcription	Fetal Kidney	kidney
12	chr4:76837800-76860800	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:76837800-76860800	Weak transcription	NH-A	brain
14	chr4:76838600-76860800	Weak transcription	NHLF	lung
15	chr4:76839000-76860400	Weak transcription	HUVEC	blood vessel
16	chr4:76839400-76860800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:76839600-76859200	Weak transcription	Brain Substantia Nigra	brain
18	chr4:76839800-76860800	Weak transcription	Psoas Muscle	Psoas
19	chr4:76839800-76860800	Weak transcription	HMEC	breast
20	chr4:76841800-76860800	Weak transcription	Brain Germinal Matrix	brain
21	chr4:76842000-76860400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:76842400-76860800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:76842600-76860800	Weak transcription	Pancreas	Pancrea
24	chr4:76843000-76860600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:76843000-76860800	Weak transcription	Thymus	Thymus
26	chr4:76843000-76860800	Weak transcription	NHEK	skin
27	chr4:76843400-76859800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:76843400-76860000	Weak transcription	A549	lung
29	chr4:76843400-76861000	Weak transcription	Small Intestine	intestine
30	chr4:76845400-76860800	Weak transcription	Right Ventricle	heart
31	chr4:76845600-76860800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:76846000-76860800	Weak transcription	HSMMtube	muscle
33	chr4:76849200-76858000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr4:76849200-76859800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:76850800-76860800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:76851800-76859000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:76852200-76860200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:76852200-76860400	Weak transcription	Primary B cells from cord blood	blood
39	chr4:76852200-76860600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:76852200-76860600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:76852200-76860600	Weak transcription	Brain Anterior Caudate	brain
42	chr4:76852200-76860600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:76852200-76860800	Weak transcription	Fetal Stomach	stomach
44	chr4:76852200-76860800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:76852400-76859600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:76852400-76860200	Weak transcription	Spleen	Spleen
47	chr4:76852400-76860400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr4:76852400-76860400	Weak transcription	Esophagus	oesophagus
49	chr4:76852400-76860600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:76852400-76860600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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