Variant report

Variant	rs13082557
Chromosome Location	chr3:119420914-119420915
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10934496	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11917710	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13092631	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34205825	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34605021	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34845376	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35010368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35012220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35141348	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35228066	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35403027	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35647314	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35864899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35918837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35931410	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4234664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4444744	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4544652	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687877	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4688028	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688029	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67287047	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771837	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778570	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786722	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6801778	1.00[CEU][hapmap];1.00[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]
rs71325399	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72963166	0.95[AFR][1000 genomes]
rs7612861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs7612954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613408	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7615769	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7617287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624404	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7634701	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7644545	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9847068	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9848716	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[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	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv591391	chr3:119403145-119442572	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13082557	C3orf15	cis	lymphoblastoid	seeQTL
rs13082557	MAATS1	cis	Skin Sun Exposed Lower leg	GTEx
rs13082557	C3orf15	cis	multi-tissue	Pritchard
rs13082557	MAATS1	cis	Stomach	GTEx
rs13082557	MAATS1	cis	Artery Tibial	GTEx
rs13082557	MAATS1	cis	Thyroid	GTEx
rs13082557	COX17	cis	lymphoblastoid	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119406000-119421400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119418400-119421200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:119418400-119422200	ZNF genes & repeats	GM12878-XiMat	blood
4	chr3:119418800-119421400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:119419000-119421200	Enhancers	Adipose Nuclei	Adipose
6	chr3:119419000-119421200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr3:119419000-119421400	Enhancers	Primary B cells from peripheral blood	blood
8	chr3:119419000-119421400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:119419000-119421400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:119419000-119421400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:119419000-119421400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:119419200-119421200	Enhancers	Duodenum Mucosa	Duodenum
13	chr3:119419200-119421400	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr3:119419200-119421400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:119419400-119421200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:119419400-119421400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:119419400-119421400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr3:119419400-119421400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr3:119419400-119421400	Weak transcription	Stomach Mucosa	stomach
20	chr3:119419600-119421200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:119419600-119421200	Weak transcription	Right Ventricle	heart
22	chr3:119419600-119421200	Weak transcription	A549	lung
23	chr3:119419600-119421400	Enhancers	Liver	Liver
24	chr3:119419800-119421400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:119420200-119421200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:119420200-119421200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:119420400-119421200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:119420400-119421200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr3:119420400-119421200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:119420400-119421200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:119420400-119421200	Enhancers	Osteobl	bone
32	chr3:119420600-119421000	Weak transcription	Spleen	Spleen
33	chr3:119420600-119421000	Weak transcription	HUVEC	blood vessel
34	chr3:119420600-119421200	Weak transcription	Primary B cells from cord blood	blood
35	chr3:119420600-119421200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr3:119420600-119421200	Weak transcription	Ovary	ovary
37	chr3:119420600-119421400	Weak transcription	Placenta	Placenta
38	chr3:119420800-119421000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr3:119420800-119421200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr3:119420800-119421200	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr3:119420800-119421200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:119420800-119421200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:119420800-119421200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:119420800-119421200	Weak transcription	Esophagus	oesophagus
45	chr3:119420800-119421200	Weak transcription	Left Ventricle	heart
46	chr3:119420800-119421400	Weak transcription	Small Intestine	intestine

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