Variant report

Variant	rs13118503
Chromosome Location	chr4:76860470-76860471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:76860400-76860550	HBMEC	blood vessel:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:76597293..76598968-chr4:76860443..76862946,2	K562	blood:
2	chr4:76860116..76861672-chr4:77068138..77069757,2	MCF-7	breast:
3	chr4:76860117..76861999-chr4:76911234..76914144,3	K562	blood:
4	chr4:76857067..76859381-chr4:76860422..76862398,2	K562	blood:
5	chr4:76859621..76862443-chr4:76895909..76899158,3	K562	blood:

No data

Variant related genes	Relation type
NAAA	TF binding region
ENSG00000138750	Chromatin interaction
ENSG00000138757	Chromatin interaction
ENSG00000198301	Chromatin interaction
ENSG00000138744	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10007919	0.88[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs10009947	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10021434	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10031733	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10031983	0.87[CEU][hapmap]
rs10518143	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12374321	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12374370	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13105416	0.82[EUR][1000 genomes]
rs13111494	0.88[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs13112512	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13129896	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13130917	0.88[CEU][hapmap]
rs17001247	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1857821	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242470	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271528	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276886	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28375800	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28422144	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28451731	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28532601	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28535831	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28588114	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28595360	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28647886	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2869462	0.94[CEU][hapmap];0.86[CHB][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34630680	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34740469	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733238	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796484	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4241577	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4859567	0.94[CEU][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4859568	0.82[EUR][1000 genomes]
rs4859569	0.82[EUR][1000 genomes]
rs4859570	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859571	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859572	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859573	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859577	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859578	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859580	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859609	0.87[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs55876513	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66498356	0.96[ASN][1000 genomes]
rs6847815	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs884004	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9994667	0.88[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]

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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs13118503	NAAA	cis	Esophagus Muscularis	GTEx
rs13118503	NAAA	cis	Muscle Skeletal	GTEx
rs13118503	NAAA	cis	Whole Blood	GTEx
rs13118503	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs13118503	NAAA	cis	Artery Aorta	GTEx
rs13118503	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs13118503	NAAA	cis	parietal	SCAN
rs13118503	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs13118503	RCHY1	cis	cerebellum	SCAN
rs13118503	NAAA	cis	cerebellum	SCAN
rs13118503	NAAA	cis	Esophagus Mucosa	GTEx
rs13118503	CDKL2	cis	parietal	SCAN
rs13118503	NAAA	cis	lymphoblastoid	seeQTL
rs13118503	NAAA	cis	Adipose Subcutaneous	GTEx
rs13118503	FAM47E	cis	cerebellum	SCAN
rs13118503	CXCL10	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76833800-76860800	Weak transcription	Fetal Heart	heart
2	chr4:76837200-76860800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:76837200-76860800	Weak transcription	HSMM	muscle
4	chr4:76837600-76860800	Weak transcription	Fetal Kidney	kidney
5	chr4:76837800-76860800	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:76837800-76860800	Weak transcription	NH-A	brain
7	chr4:76838600-76860800	Weak transcription	NHLF	lung
8	chr4:76839400-76860800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:76839800-76860800	Weak transcription	Psoas Muscle	Psoas
10	chr4:76839800-76860800	Weak transcription	HMEC	breast
11	chr4:76841800-76860800	Weak transcription	Brain Germinal Matrix	brain
12	chr4:76842400-76860800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:76842600-76860800	Weak transcription	Pancreas	Pancrea
14	chr4:76843000-76860600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:76843000-76860800	Weak transcription	Thymus	Thymus
16	chr4:76843000-76860800	Weak transcription	NHEK	skin
17	chr4:76843400-76861000	Weak transcription	Small Intestine	intestine
18	chr4:76845400-76860800	Weak transcription	Right Ventricle	heart
19	chr4:76845600-76860800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:76846000-76860800	Weak transcription	HSMMtube	muscle
21	chr4:76850800-76860800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:76852200-76860600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:76852200-76860600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:76852200-76860600	Weak transcription	Brain Anterior Caudate	brain
25	chr4:76852200-76860600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr4:76852200-76860800	Weak transcription	Fetal Stomach	stomach
27	chr4:76852200-76860800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr4:76852400-76860600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:76852400-76860600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:76852400-76860800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:76852400-76860800	Weak transcription	Brain Angular Gyrus	brain
32	chr4:76852400-76860800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:76852400-76860800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:76852400-76860800	Weak transcription	Fetal Thymus	thymus
35	chr4:76852400-76860800	Weak transcription	Ovary	ovary
36	chr4:76852400-76861000	Weak transcription	Aorta	Aorta
37	chr4:76852400-76861000	Weak transcription	Gastric	stomach
38	chr4:76852400-76861000	Weak transcription	Lung	lung
39	chr4:76852800-76860800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:76853200-76860600	Weak transcription	Placenta	Placenta
41	chr4:76857200-76860600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:76857200-76860800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:76857400-76860800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:76857400-76861000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:76857800-76860600	Weak transcription	Adipose Nuclei	Adipose
46	chr4:76857800-76860800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:76858000-76860800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr4:76858000-76860800	Weak transcription	Liver	Liver
49	chr4:76858200-76860600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:76858200-76860800	Weak transcription	Osteobl	bone

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