Variant report

Variant	rs13121161
Chromosome Location	chr4:76981544-76981545
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10002977	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10007919	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10029157	0.88[EUR][1000 genomes]
rs10031983	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12649185	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12651402	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28655366	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28818603	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28897072	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35882473	0.84[EUR][1000 genomes]
rs4429750	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859609	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6841333	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7688312	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994667	0.90[EUR][1000 genomes];0.88[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
rs13121161	NAAA	cis	Whole Blood	GTEx
rs13121161	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs13121161	NAAA	cis	Muscle Skeletal	GTEx
rs13121161	NAAA	cis	Esophagus Mucosa	GTEx
rs13121161	NAAA	cis	Esophagus Muscularis	GTEx
rs13121161	NAAA	cis	Adipose Subcutaneous	GTEx
rs13121161	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs13121161	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs13121161	NAAA	cis	Artery Aorta	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76977400-76981600	Weak transcription	Primary B cells from peripheral blood	blood
2	chr4:76978000-76982800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr4:76979400-76982200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:76979800-76982400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:76980000-76983200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr4:76980200-76981600	Enhancers	Liver	Liver
7	chr4:76980600-76981800	Enhancers	Stomach Mucosa	stomach
8	chr4:76980600-76984200	Enhancers	Primary B cells from cord blood	blood
9	chr4:76980800-76982000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr4:76980800-76982800	Enhancers	Hela-S3	cervix
11	chr4:76981000-76982000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:76981000-76982800	Enhancers	NHEK	skin
13	chr4:76981200-76982000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:76981200-76983000	Enhancers	HMEC	breast
15	chr4:76981400-76981800	Enhancers	Duodenum Mucosa	Duodenum
16	chr4:76981400-76982000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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