Variant report

Variant	rs7617537
Chromosome Location	chr3:139395785-139395786
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139395742..139397404-chr3:139400797..139402363,2	K562	blood:

Variant related genes	Relation type
ENSG00000261763	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10935341	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12186041	1.00[ASN][1000 genomes]
rs12632145	0.90[ASN][1000 genomes]
rs12634170	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074121	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16849303	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16849305	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16849307	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16849309	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35449667	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35657101	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922940	1.00[ASN][1000 genomes]
rs4474999	0.84[ASN][1000 genomes]
rs4518082	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535184	1.00[ASN][1000 genomes]
rs4549242	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4615039	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56711752	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57304307	1.00[ASN][1000 genomes]
rs59476496	0.94[ASN][1000 genomes]
rs62270189	0.90[ASN][1000 genomes]
rs62270193	0.90[ASN][1000 genomes]
rs62273120	0.97[ASN][1000 genomes]
rs62273121	0.97[ASN][1000 genomes]
rs62273122	0.94[ASN][1000 genomes]
rs6808215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71627866	0.87[ASN][1000 genomes]
rs7636269	1.00[ASN][1000 genomes]
rs7651551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289581	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810042	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9810049	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815708	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833539	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9836944	0.87[ASN][1000 genomes]
rs9848375	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865942	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871543	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878498	0.81[EUR][1000 genomes];1.00[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
rs7617537	NMNAT3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139375600-139395800	Weak transcription	Adipose Nuclei	Adipose
2	chr3:139384400-139396000	Weak transcription	Left Ventricle	heart
3	chr3:139388800-139396000	Weak transcription	Lung	lung
4	chr3:139389000-139395800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:139392000-139395800	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:139392000-139395800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:139392600-139395800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:139393000-139395800	Weak transcription	Psoas Muscle	Psoas
9	chr3:139393400-139395800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:139393400-139396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:139394000-139396000	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:139394200-139395800	Enhancers	Fetal Muscle Leg	muscle
13	chr3:139394200-139396000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:139394400-139396000	Weak transcription	NHEK	skin
15	chr3:139394600-139395800	Enhancers	Brain Angular Gyrus	brain
16	chr3:139394600-139396000	Enhancers	Pancreas	Pancrea
17	chr3:139394600-139396200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:139394800-139395800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:139394800-139395800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:139394800-139396000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
21	chr3:139394800-139396000	Weak transcription	Fetal Brain Female	brain
22	chr3:139395000-139396000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr3:139395200-139396000	Enhancers	Primary hematopoietic stem cells	blood
24	chr3:139395200-139396000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr3:139395200-139396000	Enhancers	Fetal Heart	heart
26	chr3:139395200-139396000	Enhancers	Right Ventricle	heart
27	chr3:139395200-139396200	Enhancers	Spleen	Spleen
28	chr3:139395200-139396800	Enhancers	Fetal Brain Male	brain
29	chr3:139395400-139395800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:139395400-139395800	Flanking Active TSS	Brain Germinal Matrix	brain
31	chr3:139395400-139395800	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr3:139395400-139395800	Enhancers	Fetal Intestine Large	intestine
33	chr3:139395400-139395800	Enhancers	Hela-S3	cervix
34	chr3:139395400-139395800	Enhancers	HepG2	liver
35	chr3:139395400-139395800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr3:139395400-139396400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr3:139395400-139396400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr3:139395600-139395800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr3:139395600-139395800	Active TSS	Brain Anterior Caudate	brain
40	chr3:139395600-139395800	Enhancers	Colon Smooth Muscle	Colon
41	chr3:139395600-139395800	Flanking Active TSS	Ovary	ovary
42	chr3:139395600-139395800	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr3:139395600-139395800	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr3:139395600-139396000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr3:139395600-139396000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:139395600-139396000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:139395600-139396000	Enhancers	Esophagus	oesophagus
48	chr3:139395600-139396000	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr3:139395600-139396000	Enhancers	Thymus	Thymus
50	chr3:139395600-139396200	Flanking Active TSS	Fetal Intestine Small	intestine

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