Variant report

Variant	rs7688312
Chromosome Location	chr4:76978302-76978303
allele	C/G
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];1.00[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	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13121161	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28818603	0.87[AFR][1000 genomes];0.86[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	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859609	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6841333	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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
rs7688312	NAAA	cis	Esophagus Mucosa	GTEx
rs7688312	NAAA	cis	Muscle Skeletal	GTEx
rs7688312	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs7688312	NAAA	cis	Esophagus Muscularis	GTEx
rs7688312	NAAA	cis	Adipose Subcutaneous	GTEx
rs7688312	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs7688312	NAAA	cis	Whole Blood	GTEx
rs7688312	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs7688312	NAAA	cis	Artery Aorta	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76975400-76979200	Weak transcription	HMEC	breast
2	chr4:76976000-76979800	Weak transcription	Fetal Intestine Small	intestine
3	chr4:76976000-76980800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:76976200-76979800	Weak transcription	Fetal Intestine Large	intestine
5	chr4:76976200-76980000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr4:76976400-76980200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:76976600-76979400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:76976600-76979400	Weak transcription	Stomach Mucosa	stomach
9	chr4:76976600-76980600	Weak transcription	Primary B cells from cord blood	blood
10	chr4:76977000-76979400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:76977200-76979400	Weak transcription	NHEK	skin
12	chr4:76977200-76980000	Weak transcription	K562	blood
13	chr4:76977400-76981600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:76977800-76978800	Weak transcription	GM12878-XiMat	blood
15	chr4:76978000-76982800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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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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