Variant report

Variant	rs4305683
Chromosome Location	chr5:145165324-145165325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10463270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12173238	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1654149	0.89[EUR][1000 genomes]
rs1821250	0.83[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs1897545	0.83[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs338887	0.85[TSI][hapmap]
rs338888	0.90[TSI][hapmap]
rs338890	0.82[EUR][1000 genomes]
rs338891	0.89[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs338892	0.82[CEU][hapmap]
rs338893	0.91[CEU][hapmap];0.95[TSI][hapmap]
rs338894	0.81[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs338895	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs338896	0.85[TSI][hapmap]
rs338897	0.85[TSI][hapmap]
rs4304121	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs4460183	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4628045	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs587224	0.83[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs6580387	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs677498	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs680626	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6861326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6871209	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs6892276	0.83[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021851	chr5:145106686-145187560	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4305683	SPINK5	cis	parietal	SCAN
rs4305683	SPINK1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145105400-145179000	Weak transcription	Pancreas	Pancrea
2	chr5:145109400-145194400	Weak transcription	Colonic Mucosa	Colon
3	chr5:145111400-145166800	Weak transcription	K562	blood
4	chr5:145139000-145165400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:145141200-145194400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:145148800-145166600	Weak transcription	Fetal Heart	heart
7	chr5:145152000-145167200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:145152200-145171000	Weak transcription	Stomach Mucosa	stomach
9	chr5:145154600-145166600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:145154600-145169600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:145155400-145167200	Weak transcription	Right Atrium	heart
12	chr5:145156000-145171400	Weak transcription	Aorta	Aorta
13	chr5:145156400-145166000	Weak transcription	Fetal Lung	lung
14	chr5:145156400-145167200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:145157000-145167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:145157000-145167800	Weak transcription	NH-A	brain
17	chr5:145157200-145166800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:145157400-145167200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:145157600-145167200	Weak transcription	Left Ventricle	heart
20	chr5:145158400-145167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:145158400-145171400	Weak transcription	Fetal Stomach	stomach
22	chr5:145158400-145176800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:145158400-145177000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:145158400-145179000	Weak transcription	Gastric	stomach
25	chr5:145158400-145196400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:145158400-145207000	Weak transcription	Esophagus	oesophagus
27	chr5:145158600-145165400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:145158600-145165400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:145160800-145166800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:145161000-145166000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:145161000-145176600	Weak transcription	HUVEC	blood vessel
32	chr5:145161000-145183400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:145162800-145165400	Weak transcription	Ovary	ovary
34	chr5:145162800-145166400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:145162800-145166600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:145162800-145171400	Weak transcription	Lung	lung
37	chr5:145162800-145198200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:145162800-145212800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:145163000-145166800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:145163000-145167000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:145163600-145170000	Weak transcription	Fetal Intestine Large	intestine
42	chr5:145163800-145167200	Weak transcription	Fetal Intestine Small	intestine
43	chr5:145164200-145172600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:145165000-145167800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr5:145165200-145165800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links