Variant report

Variant	rs28409655
Chromosome Location	chr4:48391379-48391380
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10003230	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10026398	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10805168	0.80[ASN][1000 genomes]
rs1117010	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12503644	0.90[ASN][1000 genomes]
rs12507206	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12511991	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12645951	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12649527	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12649528	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13105385	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13115295	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13133788	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13148849	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13150017	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1352433	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1352434	0.80[ASN][1000 genomes]
rs1586540	0.83[ASN][1000 genomes]
rs1703973	0.83[EUR][1000 genomes]
rs1948167	0.83[ASN][1000 genomes]
rs2029348	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291474	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291475	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2353312	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2353314	0.80[ASN][1000 genomes]
rs2353315	0.87[ASN][1000 genomes]
rs34975258	0.87[ASN][1000 genomes]
rs35758434	0.83[ASN][1000 genomes]
rs368609	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs372825	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3828496	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs392187	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs403495	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs404348	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs411261	0.83[EUR][1000 genomes]
rs421336	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs421833	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs432927	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs445892	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs449376	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs450498	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4694895	0.83[ASN][1000 genomes]
rs62309425	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6447634	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447635	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816010	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816352	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6821277	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6829705	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6836010	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6837335	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6844211	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6848073	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6848395	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7438704	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7668529	0.82[EUR][1000 genomes]
rs7672892	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7674269	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7678164	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs923372	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs923373	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9291323	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974014	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974015	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974016	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996532	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv528084	chr4:48387851-48413919	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28409655	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
2	chr4:48363400-48405400	Weak transcription	Right Ventricle	heart
3	chr4:48371400-48395400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:48372600-48426800	Weak transcription	Small Intestine	intestine
5	chr4:48377800-48405000	Weak transcription	Esophagus	oesophagus
6	chr4:48377800-48423800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:48378000-48423800	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:48378200-48398400	Weak transcription	A549	lung
9	chr4:48378400-48395200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:48378400-48405000	Weak transcription	Gastric	stomach
11	chr4:48378400-48405200	Weak transcription	Psoas Muscle	Psoas
12	chr4:48378600-48395200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:48379600-48391800	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:48379600-48393600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:48379600-48400200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:48380000-48392000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:48380000-48399200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr4:48381400-48405000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:48381600-48405000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:48382200-48398600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:48382200-48431800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:48383000-48397200	Strong transcription	Fetal Thymus	thymus
23	chr4:48383000-48398400	Weak transcription	Fetal Brain Female	brain
24	chr4:48383000-48405200	Weak transcription	Spleen	Spleen
25	chr4:48383200-48397000	Weak transcription	HUVEC	blood vessel
26	chr4:48383200-48398800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr4:48383200-48412000	Weak transcription	Fetal Brain Male	brain
28	chr4:48383600-48398600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:48383800-48395400	Weak transcription	HSMMtube	muscle
30	chr4:48383800-48397400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:48383800-48398000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:48384200-48403000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:48384600-48395600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr4:48384600-48396000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr4:48385000-48404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:48385200-48394800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:48385200-48395000	Weak transcription	Fetal Intestine Small	intestine
38	chr4:48385200-48395000	Weak transcription	Fetal Stomach	stomach
39	chr4:48385200-48398600	Weak transcription	Brain Angular Gyrus	brain
40	chr4:48385200-48405000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:48385200-48405000	Weak transcription	Lung	lung
42	chr4:48385200-48405400	Weak transcription	Pancreas	Pancrea
43	chr4:48385400-48422000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:48385800-48395000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:48386000-48399000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:48386600-48391400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr4:48387000-48422200	Weak transcription	Colonic Mucosa	Colon
48	chr4:48387400-48398000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:48387400-48424800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:48387600-48398600	Weak transcription	Fetal Kidney	kidney

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