Variant report

Variant	rs16849307
Chromosome Location	chr3:139393833-139393834
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	chr3:139392662..139394391-chr3:139394909..139396842,2	K562	blood:

Variant related genes	Relation type
ENSG00000163864	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10935341	0.94[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	0.88[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13074121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849303	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849309	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35449667	0.99[ASN][1000 genomes]
rs35657101	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3922940	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4474999	0.83[ASN][1000 genomes]
rs4518082	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][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	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71627866	0.86[ASN][1000 genomes]
rs7617537	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7636269	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7651551	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289581	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.99[ASN][1000 genomes]
rs9810042	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];0.97[ASN][1000 genomes]
rs9810049	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9815708	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9833539	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]
rs9836944	0.86[ASN][1000 genomes]
rs9848375	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865942	0.99[ASN][1000 genomes]
rs9871543	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874829	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.84[TSI][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16849307	NMNAT3	cis	lymphoblastoid	seeQTL
rs16849307	NMNAT3	cis	Esophagus Muscularis	GTEx
rs16849307	NMNAT3	cis	multi-tissue	Pritchard

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139369800-139395200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:139374200-139394000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:139374200-139395600	Weak transcription	Gastric	stomach
4	chr3:139374400-139394600	Weak transcription	Pancreas	Pancrea
5	chr3:139374400-139394800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:139375400-139394400	Weak transcription	Brain Anterior Caudate	brain
7	chr3:139375400-139395600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:139375600-139395800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:139380400-139394800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:139383200-139395600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:139384000-139394400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:139384400-139396000	Weak transcription	Left Ventricle	heart
13	chr3:139388800-139396000	Weak transcription	Lung	lung
14	chr3:139389000-139395800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:139389800-139394600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:139390200-139395000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:139390400-139395400	Enhancers	Brain Germinal Matrix	brain
18	chr3:139391800-139394000	Weak transcription	Brain Angular Gyrus	brain
19	chr3:139392000-139395400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:139392000-139395800	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:139392000-139395800	Weak transcription	Brain Substantia Nigra	brain
22	chr3:139392200-139394000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:139392200-139394800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:139392400-139395200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:139392600-139395800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:139393000-139394200	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:139393000-139394800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:139393000-139395600	Weak transcription	Primary T cells from cord blood	blood
29	chr3:139393000-139395800	Weak transcription	Psoas Muscle	Psoas
30	chr3:139393200-139394000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:139393200-139394600	Enhancers	Fetal Brain Male	brain
32	chr3:139393400-139395000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:139393400-139395600	Weak transcription	Fetal Intestine Small	intestine
34	chr3:139393400-139395800	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr3:139393400-139396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:139393600-139394400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
37	chr3:139393600-139394400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
38	chr3:139393600-139394400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:139393600-139394400	Enhancers	NHEK	skin
40	chr3:139393600-139394800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
41	chr3:139393600-139394800	Enhancers	Fetal Brain Female	brain
42	chr3:139393600-139395600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:139393800-139394200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
44	chr3:139393800-139394400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:139393800-139394600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:139393800-139394800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
47	chr3:139393800-139395200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr3:139393800-139395600	Enhancers	Ovary	ovary
49	chr3:139393800-139395600	Enhancers	K562	blood

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