Variant report

Variant	rs9833539
Chromosome Location	chr3:139394788-139394789
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10935341	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12186041	0.99[ASN][1000 genomes]
rs12632145	0.90[ASN][1000 genomes]
rs12634170	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13074121	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16849303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16849305	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16849307	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16849309	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35449667	0.99[ASN][1000 genomes]
rs35657101	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3922940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4474999	0.83[ASN][1000 genomes]
rs4518082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4535184	0.99[ASN][1000 genomes]
rs4549242	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4615039	0.99[ASN][1000 genomes]
rs56711752	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57304307	0.99[ASN][1000 genomes]
rs59476496	0.93[ASN][1000 genomes]
rs62270189	0.90[ASN][1000 genomes]
rs62270193	0.90[ASN][1000 genomes]
rs62273120	0.96[ASN][1000 genomes]
rs62273121	0.96[ASN][1000 genomes]
rs62273122	0.93[ASN][1000 genomes]
rs6808215	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71627866	0.86[ASN][1000 genomes]
rs7617537	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7636269	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7651551	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289581	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9810042	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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9810049	0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9815708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9836944	0.86[ASN][1000 genomes]
rs9848375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865942	0.99[ASN][1000 genomes]
rs9871543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874829	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs9878498	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9833539	NMNAT3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139369800-139395200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:139374200-139395600	Weak transcription	Gastric	stomach
3	chr3:139374400-139394800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:139375400-139395600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:139375600-139395800	Weak transcription	Adipose Nuclei	Adipose
6	chr3:139380400-139394800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:139383200-139395600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:139384400-139396000	Weak transcription	Left Ventricle	heart
9	chr3:139388800-139396000	Weak transcription	Lung	lung
10	chr3:139389000-139395800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:139390200-139395000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:139390400-139395400	Enhancers	Brain Germinal Matrix	brain
13	chr3:139392000-139395400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:139392000-139395800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:139392000-139395800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:139392200-139394800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:139392400-139395200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:139392600-139395800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:139393000-139394800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:139393000-139395600	Weak transcription	Primary T cells from cord blood	blood
21	chr3:139393000-139395800	Weak transcription	Psoas Muscle	Psoas
22	chr3:139393400-139395000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:139393400-139395600	Weak transcription	Fetal Intestine Small	intestine
24	chr3:139393400-139395800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:139393400-139396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:139393600-139394800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
27	chr3:139393600-139394800	Enhancers	Fetal Brain Female	brain
28	chr3:139393600-139395600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:139393800-139394800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
30	chr3:139393800-139395200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
31	chr3:139393800-139395600	Enhancers	Ovary	ovary
32	chr3:139393800-139395600	Enhancers	K562	blood
33	chr3:139394000-139394800	Enhancers	Fetal Heart	heart
34	chr3:139394000-139395000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr3:139394000-139396000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr3:139394200-139395000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:139394200-139395600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:139394200-139395800	Enhancers	Fetal Muscle Leg	muscle
39	chr3:139394200-139396000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:139394400-139394800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr3:139394400-139395000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:139394400-139395000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
43	chr3:139394400-139395200	Enhancers	Brain Anterior Caudate	brain
44	chr3:139394400-139395400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr3:139394400-139395400	Weak transcription	Fetal Intestine Large	intestine
46	chr3:139394400-139396000	Weak transcription	NHEK	skin
47	chr3:139394600-139394800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
48	chr3:139394600-139395000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:139394600-139395000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:139394600-139395200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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