Variant report

Variant	rs13329084
Chromosome Location	chr15:44151063-44151064
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10438303	0.87[CEU][hapmap]
rs11852767	0.93[EUR][1000 genomes]
rs11856495	0.98[EUR][1000 genomes]
rs11856795	0.85[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12440573	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs12441127	0.87[CEU][hapmap]
rs12441861	0.87[CEU][hapmap]
rs12441984	0.87[CEU][hapmap];0.98[EUR][1000 genomes]
rs12442297	0.87[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12702	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs16950562	0.87[CEU][hapmap]
rs16965120	0.87[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs16977724	0.87[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs16977798	0.87[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1965794	0.93[EUR][1000 genomes]
rs1965795	0.91[EUR][1000 genomes]
rs2228368	0.92[EUR][1000 genomes]
rs2277531	0.85[CEU][hapmap]
rs2467402	0.85[CEU][hapmap]
rs2788	0.87[CEU][hapmap]
rs28413704	0.98[EUR][1000 genomes]
rs28413881	0.91[EUR][1000 genomes]
rs28437196	0.84[EUR][1000 genomes]
rs28476182	0.96[EUR][1000 genomes]
rs28509275	0.87[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs28513374	1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs28519630	0.98[EUR][1000 genomes]
rs28524541	0.98[EUR][1000 genomes]
rs28531819	0.98[EUR][1000 genomes]
rs28564774	0.98[EUR][1000 genomes]
rs28583806	0.92[EUR][1000 genomes]
rs28590651	0.92[EUR][1000 genomes]
rs28636829	0.87[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs28674750	0.92[EUR][1000 genomes]
rs28679673	0.98[EUR][1000 genomes]
rs28684672	0.87[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs28687459	0.98[EUR][1000 genomes]
rs28696802	0.98[EUR][1000 genomes]
rs28699233	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28707214	0.98[EUR][1000 genomes]
rs28780699	0.98[EUR][1000 genomes]
rs28781888	0.92[EUR][1000 genomes]
rs28823973	0.95[EUR][1000 genomes]
rs28858500	0.95[EUR][1000 genomes]
rs28866846	0.98[EUR][1000 genomes]
rs3736180	0.87[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs3742982	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs3759790	0.87[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs3759791	0.87[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs3784275	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816792	0.87[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs3825783	0.87[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs3862142	0.85[CEU][hapmap]
rs4597285	0.90[EUR][1000 genomes]
rs4997480	0.87[CEU][hapmap]
rs56008017	0.92[EUR][1000 genomes]
rs56909447	0.95[EUR][1000 genomes]
rs61390361	0.95[EUR][1000 genomes]
rs67541383	0.93[EUR][1000 genomes]
rs678513	0.83[TSI][hapmap]
rs68079546	0.98[EUR][1000 genomes]
rs7169322	0.87[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7169988	0.87[CEU][hapmap]
rs7170751	0.98[EUR][1000 genomes]
rs7171750	0.86[CEU][hapmap]
rs7174208	0.87[CEU][hapmap]
rs7175032	0.87[CEU][hapmap]
rs7179388	0.98[EUR][1000 genomes]
rs7181039	0.87[CEU][hapmap];0.95[EUR][1000 genomes]
rs7183809	0.98[EUR][1000 genomes]
rs8023458	0.87[CEU][hapmap]
rs8023508	0.85[TSI][hapmap]
rs8032649	0.87[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs8033995	0.87[CEU][hapmap]
rs8040839	0.90[EUR][1000 genomes]
rs9944216	0.87[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs9989313	0.87[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs13329084	ELL3	cis	lymphoblastoid	seeQTL
rs13329084	ADAL	cis	lung	GTEx
rs13329084	SERF2	cis	lymphoblastoid	seeQTL
rs13329084	CKMT1A	cis	Esophagus Mucosa	GTEx
rs13329084	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs13329084	ADAL	cis	Adipose Subcutaneous	GTEx
rs13329084	CATSPER2	cis	multi-tissue	Pritchard
rs13329084	ADAL	cis	Nerve Tibial	GTEx
rs13329084	LOC440278	cis	multi-tissue	Pritchard
rs13329084	ADAL	cis	Artery Tibial	GTEx
rs13329084	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs13329084	ADAL	cis	Esophagus Muscularis	GTEx
rs13329084	C15orf63	cis	lymphoblastoid	seeQTL
rs13329084	ADAL	cis	multi-tissue	Pritchard
rs13329084	ADAL	cis	Thyroid	GTEx
rs13329084	ADAL	cis	Stomach	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44119600-44156400	Weak transcription	Pancreas	Pancrea
2	chr15:44119600-44166000	Weak transcription	Spleen	Spleen
3	chr15:44119600-44169400	Weak transcription	Fetal Intestine Large	intestine
4	chr15:44119600-44172800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:44119600-44181800	Weak transcription	Small Intestine	intestine
6	chr15:44119600-44183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:44119800-44166400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:44120600-44156600	Weak transcription	Fetal Brain Male	brain
9	chr15:44120600-44157800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:44120600-44158600	Weak transcription	Colonic Mucosa	Colon
11	chr15:44120600-44159600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:44120600-44161200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:44120600-44164600	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:44120600-44164600	Weak transcription	NHEK	skin
15	chr15:44120600-44165800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:44121000-44177600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:44121400-44159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:44121400-44160600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:44121600-44151200	Weak transcription	NHLF	lung
20	chr15:44122000-44157000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:44124000-44166000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:44128200-44151800	Weak transcription	Fetal Lung	lung
23	chr15:44128200-44151800	Weak transcription	Left Ventricle	heart
24	chr15:44128200-44167800	Weak transcription	Ovary	ovary
25	chr15:44128600-44167800	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:44129200-44161200	Weak transcription	Brain Substantia Nigra	brain
27	chr15:44131200-44167600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:44133000-44166000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:44135400-44157800	Weak transcription	Fetal Kidney	kidney
30	chr15:44136800-44152200	Weak transcription	Lung	lung
31	chr15:44137800-44160200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:44142200-44163800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:44142200-44164600	Weak transcription	Brain Angular Gyrus	brain
34	chr15:44142800-44154000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr15:44142800-44154000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:44142800-44156800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:44143000-44154200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:44143200-44154000	Strong transcription	Hela-S3	cervix
39	chr15:44143200-44154200	Strong transcription	Fetal Thymus	thymus
40	chr15:44144000-44151200	Weak transcription	NH-A	brain
41	chr15:44144000-44160400	Weak transcription	HSMM	muscle
42	chr15:44144200-44151200	Weak transcription	Aorta	Aorta
43	chr15:44144600-44151600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr15:44144600-44151800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:44144600-44152000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:44144800-44155800	Weak transcription	Brain Germinal Matrix	brain
47	chr15:44144800-44181000	Weak transcription	HepG2	liver
48	chr15:44145200-44155800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:44146000-44153400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:44146400-44156800	Strong transcription	Primary T cells from cord blood	blood

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