Variant report

Variant	rs1421942
Chromosome Location	chr5:52293087-52293088
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	chr5:52288695..52291271-chr5:52292952..52294743,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1047481	0.82[TSI][hapmap]
rs11745309	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs2193968	0.82[TSI][hapmap]
rs26682	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs3088365	0.82[TSI][hapmap]
rs3212391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212418	0.82[CHB][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35235	0.83[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4865756	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6450106	0.82[EUR][1000 genomes]
rs6869689	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1421942	ESM1	cis	parietal	SCAN
rs1421942	SDHA	trans	parietal	SCAN
rs1421942	ITGA2	cis	Artery Tibial	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52286200-52295400	Weak transcription	Pancreas	Pancrea
2	chr5:52286200-52300400	Weak transcription	Gastric	stomach
3	chr5:52286200-52303400	Weak transcription	Small Intestine	intestine
4	chr5:52286200-52313600	Weak transcription	Lung	lung
5	chr5:52286600-52293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:52286600-52300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:52286600-52302400	Weak transcription	Fetal Stomach	stomach
8	chr5:52286800-52294400	Weak transcription	Osteobl	bone
9	chr5:52286800-52298800	Weak transcription	Fetal Intestine Large	intestine
10	chr5:52287000-52293400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:52287000-52299400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr5:52287200-52293200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:52287200-52293400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr5:52287200-52293600	Weak transcription	Fetal Kidney	kidney
15	chr5:52289200-52311600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:52289400-52295600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:52290000-52299800	Weak transcription	NH-A	brain
18	chr5:52290600-52294400	Weak transcription	NHLF	lung
19	chr5:52290800-52293200	Enhancers	Brain Cingulate Gyrus	brain
20	chr5:52290800-52293200	Weak transcription	HUVEC	blood vessel
21	chr5:52291000-52295600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:52291400-52293600	Enhancers	Brain Substantia Nigra	brain
23	chr5:52291600-52293600	Transcr. at gene 5' and 3'	NHEK	skin
24	chr5:52291800-52293200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:52291800-52293400	Flanking Active TSS	HepG2	liver
26	chr5:52292000-52293200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:52292000-52294400	Weak transcription	NHDF-Ad	bronchial
28	chr5:52292200-52293200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:52292200-52293200	Enhancers	Fetal Brain Female	brain
30	chr5:52292200-52293600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:52292200-52295600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:52292400-52293200	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr5:52292400-52293200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:52292400-52294800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:52292400-52295200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:52292400-52299200	Weak transcription	Esophagus	oesophagus
37	chr5:52292400-52301000	Weak transcription	Spleen	Spleen
38	chr5:52292400-52303200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:52292600-52293400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:52292600-52293600	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr5:52292600-52294600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr5:52292600-52294800	Weak transcription	Hela-S3	cervix
43	chr5:52292800-52293200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:52292800-52293400	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr5:52292800-52293800	Flanking Active TSS	A549	lung
46	chr5:52293000-52293200	Enhancers	Brain Angular Gyrus	brain
47	chr5:52293000-52293200	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr5:52293000-52293200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr5:52293000-52293200	Flanking Active TSS	HMEC	breast
50	chr5:52293000-52293600	Active TSS	Rectal Mucosa Donor 29	rectum

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