Variant report

Variant	rs469523
Chromosome Location	chr5:112294680-112294681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112256942..112259777-chr5:112292490..112295980,4	MCF-7	breast:
2	chr5:112256312..112258572-chr5:112293343..112296094,6	MCF-7	breast:
3	chr5:112294256..112295877-chr5:112297212..112298935,2	K562	blood:
4	chr5:112293295..112296045-chr5:112298149..112301329,3	MCF-7	breast:
5	chr5:112292808..112297954-chr5:112311731..112314309,4	MCF-7	breast:
6	chr5:112292660..112295480-chr5:112309614..112313888,4	K562	blood:
7	chr5:112294258..112297172-chr5:112310787..112314038,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129625	Chromatin interaction
ENSG00000172795	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10515451	0.84[YRI][hapmap]
rs1093611	0.84[TSI][hapmap]
rs149130	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs149190	0.89[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs149191	0.82[ASN][1000 genomes]
rs149502	0.88[EUR][1000 genomes]
rs151979	0.89[ASN][1000 genomes]
rs151980	0.85[ASN][1000 genomes]
rs153548	0.81[MEX][hapmap]
rs153553	0.88[ASN][1000 genomes]
rs153556	0.85[ASN][1000 genomes]
rs153557	0.84[ASN][1000 genomes]
rs153561	0.82[ASN][1000 genomes]
rs153562	0.82[EUR][1000 genomes]
rs153563	0.82[ASN][1000 genomes]
rs153566	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs153568	0.95[EUR][1000 genomes]
rs153569	0.87[ASN][1000 genomes]
rs153570	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs153571	0.88[CEU][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs1625623	0.88[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1644099	0.93[ASN][1000 genomes]
rs17135222	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs173466	0.81[EUR][1000 genomes]
rs430665	0.82[TSI][hapmap]
rs467660	0.85[ASN][1000 genomes]
rs469675	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469702	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs469716	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs469753	0.95[ASN][1000 genomes]
rs712662	0.82[TSI][hapmap]
rs712665	0.82[TSI][hapmap]
rs818799	0.83[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	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs469523	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs469523	TRIM36	cis	cerebellum	SCAN
rs469523	NCRNA00219	cis	parietal	SCAN
rs469523	REEP5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112291600-112297600	Enhancers	HepG2	liver
2	chr5:112292600-112295000	Enhancers	Hela-S3	cervix
3	chr5:112292600-112295200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:112292800-112294800	Enhancers	Fetal Brain Female	brain
5	chr5:112292800-112295200	Enhancers	Adipose Nuclei	Adipose
6	chr5:112292800-112295600	Weak transcription	Lung	lung
7	chr5:112293000-112295200	Enhancers	Liver	Liver
8	chr5:112293200-112294800	Enhancers	Brain Angular Gyrus	brain
9	chr5:112293200-112295000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr5:112293200-112295200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr5:112293200-112296400	Enhancers	Stomach Smooth Muscle	stomach
12	chr5:112293200-112296400	Enhancers	HSMMtube	muscle
13	chr5:112293200-112296400	Enhancers	HUVEC	blood vessel
14	chr5:112293200-112297000	Enhancers	NHDF-Ad	bronchial
15	chr5:112293200-112297000	Enhancers	NHLF	lung
16	chr5:112293400-112297200	Enhancers	Fetal Muscle Leg	muscle
17	chr5:112293400-112297200	Enhancers	Fetal Stomach	stomach
18	chr5:112293600-112295200	Enhancers	Fetal Lung	lung
19	chr5:112293600-112296400	Enhancers	HSMM	muscle
20	chr5:112293800-112294800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr5:112293800-112294800	Enhancers	Fetal Heart	heart
22	chr5:112293800-112294800	Enhancers	Small Intestine	intestine
23	chr5:112293800-112295000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:112293800-112295000	Enhancers	Brain Hippocampus Middle	brain
25	chr5:112293800-112295200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:112293800-112295800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:112293800-112296000	Enhancers	Colon Smooth Muscle	Colon
28	chr5:112293800-112296000	Enhancers	Stomach Mucosa	stomach
29	chr5:112293800-112296000	Enhancers	HMEC	breast
30	chr5:112293800-112297000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:112293800-112297000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:112293800-112297200	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr5:112293800-112297200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr5:112293800-112297600	Enhancers	K562	blood
35	chr5:112293800-112297800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr5:112294000-112294800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr5:112294000-112294800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:112294000-112295200	Flanking Active TSS	GM12878-XiMat	blood
39	chr5:112294000-112295200	Enhancers	NHEK	skin
40	chr5:112294000-112295400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:112294000-112311800	Weak transcription	Right Atrium	heart
42	chr5:112294200-112295000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr5:112294200-112295000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:112294200-112295000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:112294200-112295000	Weak transcription	Psoas Muscle	Psoas
46	chr5:112294200-112295200	Enhancers	Brain Anterior Caudate	brain
47	chr5:112294200-112296800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr5:112294400-112294800	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr5:112294400-112294800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:112294400-112294800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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