Variant report

Variant	rs13129896
Chromosome Location	chr4:76867660-76867661
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	chr4:76866002..76869034-chr4:76870161..76872901,3	K562	blood:

Variant related genes	Relation type
ENSG00000268788	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10007919	0.81[AMR][1000 genomes]
rs10009947	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10021434	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10029157	0.81[AMR][1000 genomes]
rs10031733	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10031983	0.81[AMR][1000 genomes]
rs10518143	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12374321	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12374370	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12649185	0.81[AMR][1000 genomes]
rs13105416	0.81[EUR][1000 genomes]
rs13112512	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13118503	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17001247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1857821	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242470	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271528	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276886	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28375800	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28422144	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28451731	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28532601	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28535831	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28588114	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28595360	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28647886	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2869462	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34630680	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34740469	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733238	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796484	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4241577	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859567	0.82[EUR][1000 genomes]
rs4859568	0.81[EUR][1000 genomes]
rs4859569	0.82[EUR][1000 genomes]
rs4859570	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859571	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859572	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859573	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859577	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859578	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859580	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55876513	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66498356	0.93[ASN][1000 genomes]
rs6847815	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs884004	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9994667	0.81[AMR][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
rs13129896	NAAA	cis	Esophagus Muscularis	GTEx
rs13129896	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs13129896	NAAA	cis	Artery Aorta	GTEx
rs13129896	NAAA	cis	Adipose Subcutaneous	GTEx
rs13129896	NAAA	cis	Esophagus Mucosa	GTEx
rs13129896	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs13129896	NAAA	cis	Whole Blood	GTEx
rs13129896	NAAA	cis	Muscle Skeletal	GTEx
rs13129896	NAAA	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76862000-76868200	Weak transcription	Fetal Lung	lung
2	chr4:76862000-76871600	Weak transcription	Fetal Kidney	kidney
3	chr4:76862000-76875600	Weak transcription	Fetal Heart	heart
4	chr4:76862000-76896600	Weak transcription	Stomach Mucosa	stomach
5	chr4:76862200-76868000	Weak transcription	GM12878-XiMat	blood
6	chr4:76862200-76868200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:76862200-76871000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:76862200-76871000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:76862200-76875200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:76862200-76876400	Weak transcription	Gastric	stomach
11	chr4:76862200-76876600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:76862200-76886600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:76862400-76867800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:76862400-76868000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:76862400-76868000	Weak transcription	Lung	lung
16	chr4:76862400-76868000	Weak transcription	HUVEC	blood vessel
17	chr4:76862400-76868400	Weak transcription	Ovary	ovary
18	chr4:76862400-76868400	Weak transcription	HSMMtube	muscle
19	chr4:76862400-76868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:76862400-76873400	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:76862400-76875400	Weak transcription	Spleen	Spleen
22	chr4:76862400-76876600	Weak transcription	Aorta	Aorta
23	chr4:76862400-76876600	Weak transcription	Small Intestine	intestine
24	chr4:76862600-76867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:76862600-76867800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:76862600-76867800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:76862600-76867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:76862600-76867800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:76862600-76867800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:76862600-76867800	Weak transcription	Liver	Liver
31	chr4:76862600-76867800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr4:76862600-76867800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:76862600-76867800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr4:76862600-76867800	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:76862600-76867800	Weak transcription	Fetal Stomach	stomach
36	chr4:76862600-76867800	Weak transcription	Fetal Thymus	thymus
37	chr4:76862600-76868000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr4:76862600-76868000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:76862600-76868000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:76862600-76868000	Weak transcription	Primary B cells from cord blood	blood
41	chr4:76862600-76868000	Weak transcription	Primary T cells from cord blood	blood
42	chr4:76862600-76868000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:76862600-76868000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr4:76862600-76868000	Weak transcription	Adipose Nuclei	Adipose
45	chr4:76862600-76868000	Weak transcription	Colonic Mucosa	Colon
46	chr4:76862600-76868000	Weak transcription	Fetal Brain Female	brain
47	chr4:76862600-76868000	Weak transcription	Left Ventricle	heart
48	chr4:76862600-76868000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:76862600-76868000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:76862600-76868000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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