Variant report

Variant	rs11130344
Chromosome Location	chr3:53179915-53179916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53177843..53180443-chr3:53877021..53879242,2	MCF-7	breast:
2	chr3:53176620..53178879-chr3:53179713..53181872,2	MCF-7	breast:
3	chr3:53163425..53164926-chr3:53179286..53181203,2	K562	blood:

Variant related genes	Relation type
ENSG00000163933	Chromatin interaction
ENSG00000016391	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11130345	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130350	0.88[CHD][hapmap]
rs13085294	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1483185	0.80[CHD][hapmap]
rs2358617	0.93[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773729	0.88[CHD][hapmap]
rs4687706	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6778939	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6778964	0.90[CHD][hapmap]
rs6807359	0.83[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7616077	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[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	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11130344	GLT8D1	cis	cerebellum	SCAN
rs11130344	PBRM1	cis	cerebellum	SCAN
rs11130344	SLC38A3	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53165600-53181400	Weak transcription	Spleen	Spleen
2	chr3:53169200-53183800	Weak transcription	Right Ventricle	heart
3	chr3:53174000-53182400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:53174800-53189600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:53175000-53183800	Weak transcription	Esophagus	oesophagus
6	chr3:53175200-53183800	Weak transcription	Right Atrium	heart
7	chr3:53175400-53183600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:53175600-53180600	Weak transcription	Adipose Nuclei	Adipose
9	chr3:53175600-53184000	Weak transcription	NHDF-Ad	bronchial
10	chr3:53175800-53180600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:53175800-53183800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:53176400-53188000	Enhancers	Stomach Mucosa	stomach
13	chr3:53176600-53180800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:53177000-53180200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:53177200-53181600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:53177200-53182400	Enhancers	Pancreas	Pancrea
17	chr3:53177800-53190200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr3:53178000-53181200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:53178000-53181400	Weak transcription	GM12878-XiMat	blood
20	chr3:53178000-53181600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr3:53178000-53182200	Enhancers	Gastric	stomach
22	chr3:53178000-53189600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr3:53178200-53184400	Weak transcription	Placenta	Placenta
24	chr3:53178600-53190200	Enhancers	Colonic Mucosa	Colon
25	chr3:53179000-53180200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:53179000-53190000	Enhancers	Duodenum Mucosa	Duodenum
27	chr3:53179200-53180000	Enhancers	Hela-S3	cervix
28	chr3:53179200-53180600	Bivalent Enhancer	HepG2	liver
29	chr3:53179200-53180800	Enhancers	Fetal Intestine Small	intestine
30	chr3:53179200-53181200	Enhancers	A549	lung
31	chr3:53179200-53186400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr3:53179400-53180400	Weak transcription	Lung	lung
33	chr3:53179400-53180600	Enhancers	Fetal Intestine Large	intestine
34	chr3:53179600-53180400	Weak transcription	Small Intestine	intestine
35	chr3:53179600-53180600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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