Variant report

Variant	rs1472967
Chromosome Location	chr4:48347763-48347764
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48270465..48272288-chr4:48345369..48347780,2	MCF-7	breast:
2	chr4:48346882..48348699-chr4:48349922..48352007,2	K562	blood:

Variant related genes	Relation type
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10003230	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10026398	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10029785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1055721	0.90[YRI][hapmap]
rs10938534	0.81[JPT][hapmap]
rs11945562	0.86[JPT][hapmap]
rs12645951	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12649527	0.80[EUR][1000 genomes]
rs12649528	0.80[EUR][1000 genomes]
rs1703973	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2029348	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291474	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2291475	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2353312	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs372825	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs382335	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs392187	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs403495	0.85[ASN][1000 genomes]
rs404348	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs404445	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs404656	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs411261	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs421336	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs421833	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs429969	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs432927	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs445892	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs449376	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs450498	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62309425	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447635	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6816010	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6816352	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6821277	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6829705	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6829716	0.86[JPT][hapmap]
rs6836010	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6836632	0.86[JPT][hapmap]
rs6837335	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6844211	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6848073	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6848395	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7438704	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7654770	0.86[JPT][hapmap]
rs7664981	0.94[YRI][hapmap]
rs7668529	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678164	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7678379	0.86[JPT][hapmap]
rs7697851	0.86[JPT][hapmap]
rs7700018	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs937888	0.81[JPT][hapmap]
rs992423	0.86[JPT][hapmap]
rs9996532	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1472967	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48344800-48349000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48344800-48349200	Weak transcription	Lung	lung
3	chr4:48344800-48352200	Weak transcription	Pancreas	Pancrea
4	chr4:48344800-48354400	Weak transcription	Esophagus	oesophagus
5	chr4:48344800-48362400	Weak transcription	Gastric	stomach
6	chr4:48345000-48350000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr4:48345200-48349200	Weak transcription	Left Ventricle	heart
8	chr4:48345400-48350400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:48345600-48349400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr4:48345800-48347800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr4:48345800-48348600	Enhancers	Fetal Lung	lung
12	chr4:48345800-48348800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:48345800-48349200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:48345800-48349400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr4:48345800-48353600	Weak transcription	Spleen	Spleen
16	chr4:48345800-48356000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:48345800-48356600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr4:48346000-48348200	Weak transcription	HSMMtube	muscle
19	chr4:48346000-48348600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr4:48346000-48348600	Enhancers	HepG2	liver
21	chr4:48346000-48348800	Active TSS	GM12878-XiMat	blood
22	chr4:48346000-48349200	Enhancers	Colon Smooth Muscle	Colon
23	chr4:48346000-48349400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:48346000-48350000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr4:48346000-48350800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:48346000-48351200	Weak transcription	A549	lung
27	chr4:48346000-48353000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr4:48346000-48362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:48346200-48348000	Enhancers	NHEK	skin
30	chr4:48346200-48348200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:48346200-48348400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:48346200-48348400	Weak transcription	Hela-S3	cervix
33	chr4:48346200-48348600	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr4:48346200-48349200	Weak transcription	Ovary	ovary
35	chr4:48346200-48349400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr4:48346200-48349400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr4:48346200-48349400	Enhancers	HMEC	breast
38	chr4:48346200-48349400	Enhancers	Osteobl	bone
39	chr4:48346200-48350600	Weak transcription	Brain Anterior Caudate	brain
40	chr4:48346200-48352200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr4:48346200-48354600	Weak transcription	Fetal Intestine Small	intestine
42	chr4:48346200-48356200	Weak transcription	Fetal Thymus	thymus
43	chr4:48346200-48356600	Weak transcription	HUVEC	blood vessel
44	chr4:48346200-48358400	Weak transcription	Small Intestine	intestine
45	chr4:48346200-48362400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:48346400-48348200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:48346400-48348400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:48346400-48348400	Weak transcription	Adipose Nuclei	Adipose
49	chr4:48346400-48348400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr4:48346400-48349200	Weak transcription	Primary monocytes fromperipheralblood	blood

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