Variant report

Variant	rs1625623
Chromosome Location	chr5:112301096-112301097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112255892..112258001-chr5:112300959..112303737,2	MCF-7	breast:
2	chr5:112293295..112296045-chr5:112298149..112301329,3	MCF-7	breast:
3	chr5:112298220..112301576-chr5:112303525..112306248,4	K562	blood:
4	chr5:112299891..112302551-chr5:112304057..112307148,4	K562	blood:

Variant related genes	Relation type
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1093611	0.80[MEX][hapmap];0.80[TSI][hapmap]
rs149130	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs149190	0.94[JPT][hapmap]
rs153566	0.82[EUR][1000 genomes]
rs153568	0.87[EUR][1000 genomes]
rs153570	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs153571	0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs17135222	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs469523	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]
rs469675	0.92[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs469702	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs469716	0.88[CEU][hapmap];0.90[EUR][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	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
4	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1625623	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs1625623	REEP5	cis	Esophagus Muscularis	GTEx
rs1625623	NCRNA00219	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112294000-112311800	Weak transcription	Right Atrium	heart
2	chr5:112294800-112304400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:112295200-112304400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:112297000-112304400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:112298200-112311800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:112300000-112301600	Weak transcription	HepG2	liver
7	chr5:112300000-112305200	Weak transcription	NH-A	brain
8	chr5:112300000-112305600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:112300000-112307000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr5:112300200-112303200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:112300200-112303800	Weak transcription	A549	lung
12	chr5:112300200-112305000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr5:112300200-112305000	Weak transcription	Hela-S3	cervix
14	chr5:112300200-112305000	Weak transcription	HUVEC	blood vessel
15	chr5:112300200-112305000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr5:112300200-112311400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:112300400-112302000	Weak transcription	Placenta	Placenta
18	chr5:112300400-112303600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:112300400-112303600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:112300400-112303800	Weak transcription	K562	blood
21	chr5:112300400-112304200	Weak transcription	GM12878-XiMat	blood
22	chr5:112300400-112304600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:112300400-112305200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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