Variant report

Variant	rs13112512
Chromosome Location	chr4:76867908-76867909
allele	C/T
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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NAAA-1	chr4:76867721-76868384	ucscGeneNc_uc010iiy_1

Variant related genes	Relation type
ENSG00000268788	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10009947	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10021434	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10031733	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10518143	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12374321	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12374370	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13118503	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13129896	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17001247	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1857821	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242470	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271528	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276886	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28375800	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28422144	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28451731	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28532601	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28535831	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28588114	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28595360	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28647886	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2869462	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34630680	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34740469	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733238	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796484	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4241577	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859570	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859571	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859572	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859573	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859577	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859578	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859580	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55876513	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs66498356	0.93[ASN][1000 genomes]
rs6847815	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs884004	0.87[AMR][1000 genomes];0.89[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13112512	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs13112512	NAAA	cis	Artery Aorta	GTEx
rs13112512	NAAA	cis	Esophagus Muscularis	GTEx
rs13112512	NAAA	cis	Muscle Skeletal	GTEx
rs13112512	NAAA	cis	Esophagus Mucosa	GTEx
rs13112512	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs13112512	NAAA	cis	Adipose Subcutaneous	GTEx
rs13112512	CXCL10	Cis_1M	lymphoblastoid	RTeQTL

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	chr4:76862400-76868000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:76862400-76868000	Weak transcription	Lung	lung
15	chr4:76862400-76868000	Weak transcription	HUVEC	blood vessel
16	chr4:76862400-76868400	Weak transcription	Ovary	ovary
17	chr4:76862400-76868400	Weak transcription	HSMMtube	muscle
18	chr4:76862400-76868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:76862400-76873400	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:76862400-76875400	Weak transcription	Spleen	Spleen
21	chr4:76862400-76876600	Weak transcription	Aorta	Aorta
22	chr4:76862400-76876600	Weak transcription	Small Intestine	intestine
23	chr4:76862600-76868000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:76862600-76868000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:76862600-76868000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:76862600-76868000	Weak transcription	Primary B cells from cord blood	blood
27	chr4:76862600-76868000	Weak transcription	Primary T cells from cord blood	blood
28	chr4:76862600-76868000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:76862600-76868000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:76862600-76868000	Weak transcription	Adipose Nuclei	Adipose
31	chr4:76862600-76868000	Weak transcription	Colonic Mucosa	Colon
32	chr4:76862600-76868000	Weak transcription	Fetal Brain Female	brain
33	chr4:76862600-76868000	Weak transcription	Left Ventricle	heart
34	chr4:76862600-76868000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:76862600-76868000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:76862600-76868000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr4:76862600-76868000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:76862600-76868000	Weak transcription	HepG2	liver
39	chr4:76862600-76868000	Weak transcription	K562	blood
40	chr4:76862600-76868200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:76862600-76868200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:76862600-76868200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr4:76862600-76868200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:76862600-76868200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:76862600-76868200	Weak transcription	A549	lung
46	chr4:76862600-76868200	Weak transcription	NH-A	brain
47	chr4:76862600-76868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:76862600-76868400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr4:76862600-76868400	Weak transcription	Dnd41	blood
50	chr4:76862600-76869200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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