Variant report

Variant	rs884004
Chromosome Location	chr4:76934577-76934578
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10007919	0.94[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10009947	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10021434	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10029157	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10031733	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10031983	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10518143	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374321	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12374370	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12649185	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13111494	0.94[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap]
rs13112512	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13118503	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13129896	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13130917	0.94[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap]
rs17001247	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1857821	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242470	0.94[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271528	0.94[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276886	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28375800	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28422144	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28451731	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28532601	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28535831	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28588114	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28595360	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28647886	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2869462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34630680	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34740469	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3733238	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796484	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4241577	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4429750	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859567	0.88[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs4859570	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859571	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4859572	0.83[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859573	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859577	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859578	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859580	0.83[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859609	0.86[CHB][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs55876513	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66498356	0.83[ASN][1000 genomes]
rs6847815	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs884304	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs9994667	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs884004	NAAA	cis	Adipose Subcutaneous	GTEx
rs884004	CXCL10	cis	lymphoblastoid	seeQTL
rs884004	NAAA	cis	Muscle Skeletal	GTEx
rs884004	RCHY1	cis	cerebellum	SCAN
rs884004	NAAA	cis	Whole Blood	GTEx
rs884004	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs884004	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs884004	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs884004	NAAA	cis	Esophagus Mucosa	GTEx
rs884004	CXCL10	cis	multi-tissue	Pritchard
rs884004	NAAA	cis	parietal	SCAN
rs884004	NAAA	cis	cerebellum	SCAN
rs884004	NAAA	cis	Artery Aorta	GTEx
rs884004	NAAA	cis	Esophagus Muscularis	GTEx
rs884004	FAM47E	cis	cerebellum	SCAN
rs884004	NAAA	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76932600-76935400	Enhancers	Liver	Liver
2	chr4:76933000-76937400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:76933000-76937600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:76933000-76937600	Weak transcription	Placenta	Placenta
5	chr4:76933000-76937600	Weak transcription	Pancreas	Pancrea
6	chr4:76933400-76934600	Enhancers	HMEC	breast
7	chr4:76933400-76935200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:76933400-76936000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr4:76933400-76936200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr4:76933400-76936200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:76933400-76937600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:76933600-76934600	Enhancers	NHEK	skin
13	chr4:76933600-76934600	Enhancers	NHLF	lung
14	chr4:76933600-76935000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:76933600-76936000	Weak transcription	Primary B cells from cord blood	blood
16	chr4:76933600-76937400	Weak transcription	Fetal Thymus	thymus
17	chr4:76933600-76937600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:76933800-76934800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:76933800-76935000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:76933800-76937600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:76934000-76935000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:76934000-76935800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:76934000-76936800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:76934000-76937200	Enhancers	GM12878-XiMat	blood
25	chr4:76934000-76938000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:76934200-76934600	Enhancers	Small Intestine	intestine
27	chr4:76934200-76935000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr4:76934200-76936000	Enhancers	Fetal Intestine Small	intestine
29	chr4:76934200-76936400	Enhancers	Fetal Intestine Large	intestine
30	chr4:76934400-76934600	Enhancers	Fetal Muscle Leg	muscle
31	chr4:76934400-76937400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr4:76934400-76937400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:76934400-76937400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:76934400-76937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:76934400-76937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:76934400-76944200	Weak transcription	Primary B cells from peripheral blood	blood

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