Variant report

Variant	rs55876513
Chromosome Location	chr4:76883698-76883699
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10009947	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10021434	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10031733	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10518143	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12374321	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12374370	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13112512	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13118503	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13129896	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17001247	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1857821	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2242470	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271528	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2276886	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28375800	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28422144	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28451731	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28532601	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28535831	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28588114	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28595360	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28647886	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2869462	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34630680	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34740469	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733238	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3796484	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241577	0.81[EUR][1000 genomes]
rs4859570	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4859571	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4859572	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4859573	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4859577	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859578	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859580	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66498356	0.86[ASN][1000 genomes]
rs6847815	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs884004	0.84[AMR][1000 genomes];0.83[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs55876513	NAAA	cis	Artery Aorta	GTEx
rs55876513	NAAA	cis	Esophagus Muscularis	GTEx
rs55876513	NAAA	cis	Muscle Skeletal	GTEx
rs55876513	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs55876513	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs55876513	NAAA	cis	Esophagus Mucosa	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	chr4:76862200-76886600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:76863800-76884600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:76864600-76884800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:76864800-76883800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:76864800-76884400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:76864800-76884600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:76866400-76886800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:76867400-76885600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:76867400-76886600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:76867800-76884600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:76867800-76888800	Strong transcription	Liver	Liver
15	chr4:76867800-76900000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
17	chr4:76868000-76884600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:76868000-76884800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:76868000-76886400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:76868000-76886600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:76868000-76899800	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:76868000-76903000	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr4:76868000-76903000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
30	chr4:76869200-76900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:76870000-76886800	Strong transcription	Primary T cells from cord blood	blood
32	chr4:76870800-76885600	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr4:76870800-76897600	Strong transcription	Brain Germinal Matrix	brain
34	chr4:76871600-76886600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr4:76872200-76902800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:76873800-76884400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:76876200-76884000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:76876600-76884800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr4:76876600-76886600	Strong transcription	Primary B cells from cord blood	blood
40	chr4:76876800-76895200	Strong transcription	Fetal Kidney	kidney
41	chr4:76879200-76885000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:76879600-76884600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:76879600-76884800	Weak transcription	Fetal Brain Male	brain
44	chr4:76880000-76886600	Weak transcription	Fetal Heart	heart
45	chr4:76880600-76893400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:76881200-76884400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:76881200-76884800	Weak transcription	Brain Angular Gyrus	brain
48	chr4:76881200-76885000	Weak transcription	Hela-S3	cervix
49	chr4:76881200-76886200	Weak transcription	Gastric	stomach
50	chr4:76881200-76886400	Weak transcription	Pancreas	Pancrea

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