Variant report

Variant	rs9292000
Chromosome Location	chr5:52245138-52245139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52243208..52246085-chr5:52282017..52284486,2	MCF-7	breast:
2	chr5:52244476..52245215-chr5:52391489..52392462,3	MCF-7	breast:
3	chr5:52243837..52246026-chr5:52316094..52318313,2	MCF-7	breast:
4	chr5:52244273..52246874-chr5:52284639..52287119,3	MCF-7	breast:
5	chr5:52244780..52247572-chr5:52249796..52252128,2	K562	blood:
6	chr5:52244525..52246067-chr5:52384828..52387820,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272123	Chromatin interaction
ENSG00000164171	Chromatin interaction
ENSG00000249899	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10471826	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1047481	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1047482	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1047483	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1047485	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054085	0.81[EUR][1000 genomes]
rs10940282	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940283	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10940284	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1124141	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11745309	0.83[EUR][1000 genomes]
rs2193968	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26682	0.87[EUR][1000 genomes]
rs3088363	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3088364	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3088365	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35235	0.87[EUR][1000 genomes]
rs36000043	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764923	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6869687	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6869689	0.82[EUR][1000 genomes]
rs6890588	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6895049	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6895250	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7703316	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv1794366	chr5:52240421-52249476	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9292000	ITGA1	cis	Thyroid	GTEx
rs9292000	ITGA2	cis	Artery Tibial	GTEx
rs9292000	ITGA2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52202200-52252200	Weak transcription	Small Intestine	intestine
2	chr5:52220600-52252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:52221400-52251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:52229000-52246600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:52231600-52245400	Weak transcription	Colonic Mucosa	Colon
6	chr5:52232800-52249800	Weak transcription	Left Ventricle	heart
7	chr5:52238800-52252200	Strong transcription	Liver	Liver
8	chr5:52240000-52245400	Weak transcription	Placenta	Placenta
9	chr5:52240000-52249800	Weak transcription	Aorta	Aorta
10	chr5:52240000-52253000	Weak transcription	Right Ventricle	heart
11	chr5:52240000-52253400	Weak transcription	Esophagus	oesophagus
12	chr5:52240000-52253600	Weak transcription	Lung	lung
13	chr5:52240200-52247000	Weak transcription	Fetal Muscle Leg	muscle
14	chr5:52240200-52251800	Weak transcription	Fetal Intestine Small	intestine
15	chr5:52240200-52253400	Weak transcription	Spleen	Spleen
16	chr5:52240400-52251800	Weak transcription	Fetal Intestine Large	intestine
17	chr5:52241200-52245600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:52241200-52252000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr5:52241400-52245400	Enhancers	NHDF-Ad	bronchial
20	chr5:52241400-52247600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:52241800-52245400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:52242200-52245200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:52242400-52245200	Enhancers	HUVEC	blood vessel
24	chr5:52242400-52247600	Enhancers	NHEK	skin
25	chr5:52242600-52245600	Enhancers	NHLF	lung
26	chr5:52242600-52247600	Enhancers	HMEC	breast
27	chr5:52243200-52245200	Enhancers	HSMM	muscle
28	chr5:52243200-52245200	Enhancers	NH-A	brain
29	chr5:52243400-52245200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:52243400-52248200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:52243400-52252600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:52243600-52245200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:52243800-52246800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:52244000-52245800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:52244200-52245200	Enhancers	Hela-S3	cervix
36	chr5:52244200-52245200	Enhancers	HSMMtube	muscle
37	chr5:52244200-52247600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:52244400-52246600	Genic enhancers	Colon Smooth Muscle	Colon
39	chr5:52244400-52247000	Strong transcription	Adipose Nuclei	Adipose
40	chr5:52244400-52247400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr5:52244800-52245600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:52244800-52245600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:52244800-52246000	Strong transcription	Fetal Kidney	kidney
44	chr5:52244800-52246000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr5:52244800-52246200	Strong transcription	Fetal Lung	lung
46	chr5:52244800-52246800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:52244800-52250800	Weak transcription	HepG2	liver
48	chr5:52244800-52253600	Weak transcription	Fetal Stomach	stomach
49	chr5:52245000-52245400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:52245000-52245600	Genic enhancers	Dnd41	blood

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