Variant report

Variant	rs9884339
Chromosome Location	chr4:48403405-48403406
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	chr4:48402728..48404453-chr4:48414243..48416411,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10000288	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10001054	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10003458	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10004425	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10024547	0.86[ASN][1000 genomes]
rs1055720	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1055721	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938530	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731199	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11737752	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13122065	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13141335	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17609600	0.85[ASN][1000 genomes]
rs17655838	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1876834	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28411210	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28464394	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28636546	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28659782	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28690347	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695376	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695382	0.83[AFR][1000 genomes]
rs6447631	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447632	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66894522	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68142816	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6841390	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843652	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853315	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7655066	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7658851	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7662325	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7688310	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7700141	0.84[AFR][1000 genomes]
rs9992736	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9995939	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999482	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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
rs9884339	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 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	chr4:48372600-48426800	Weak transcription	Small Intestine	intestine
4	chr4:48377800-48405000	Weak transcription	Esophagus	oesophagus
5	chr4:48377800-48423800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:48378000-48423800	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:48378400-48405000	Weak transcription	Gastric	stomach
8	chr4:48378400-48405200	Weak transcription	Psoas Muscle	Psoas
9	chr4:48381400-48405000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:48381600-48405000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:48382200-48431800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:48383000-48405200	Weak transcription	Spleen	Spleen
13	chr4:48383200-48412000	Weak transcription	Fetal Brain Male	brain
14	chr4:48385000-48404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:48385200-48405000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:48385200-48405000	Weak transcription	Lung	lung
17	chr4:48385200-48405400	Weak transcription	Pancreas	Pancrea
18	chr4:48385400-48422000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:48387000-48422200	Weak transcription	Colonic Mucosa	Colon
20	chr4:48387400-48424800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:48387600-48431400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:48387800-48424600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:48388000-48404400	Weak transcription	HepG2	liver
24	chr4:48388000-48405200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:48388200-48405400	Weak transcription	NHEK	skin
26	chr4:48391000-48412600	Weak transcription	Brain Substantia Nigra	brain
27	chr4:48391000-48424800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr4:48391200-48405400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr4:48391200-48423200	Weak transcription	NHLF	lung
30	chr4:48391200-48424600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:48391400-48403600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:48391600-48434000	Weak transcription	Fetal Heart	heart
33	chr4:48395600-48404600	Weak transcription	Thymus	Thymus
34	chr4:48395600-48405000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:48395600-48405000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:48395600-48424800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:48395800-48404200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:48396000-48404600	Weak transcription	Fetal Stomach	stomach
39	chr4:48396000-48404800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr4:48396200-48422000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr4:48396400-48412400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr4:48397000-48424800	Weak transcription	Stomach Mucosa	stomach
43	chr4:48397400-48424000	Weak transcription	HUVEC	blood vessel
44	chr4:48398800-48404800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr4:48398800-48405000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:48398800-48423200	Weak transcription	GM12878-XiMat	blood
47	chr4:48399000-48405000	Weak transcription	Osteobl	bone
48	chr4:48399000-48422000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:48399000-48423800	Weak transcription	NH-A	brain
50	chr4:48399000-48423800	Weak transcription	NHDF-Ad	bronchial

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