Variant report

Variant	rs7972025
Chromosome Location	chr12:44222722-44222723
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:44197555..44202082-chr12:44219321..44224097,7	MCF-7	breast:
2	chr12:44220265..44224053-chr12:44227349..44231351,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139173	Chromatin interaction
ENSG00000151239	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10506231	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1057486	0.83[ASN][1000 genomes]
rs10736017	0.84[ASN][1000 genomes]
rs10748378	0.84[ASN][1000 genomes]
rs10785462	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs10785463	0.84[ASN][1000 genomes]
rs10785466	0.84[ASN][1000 genomes]
rs10880573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880578	0.87[ASN][1000 genomes]
rs10880585	0.84[ASN][1000 genomes]
rs11182273	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs11182275	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11182293	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs11182324	0.84[ASN][1000 genomes]
rs11182325	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1358705	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1406787	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1609548	0.84[ASN][1000 genomes]
rs1609549	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs1610291	0.84[ASN][1000 genomes]
rs1614042	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1621279	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1622590	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1675756	0.84[ASN][1000 genomes]
rs1675758	0.84[ASN][1000 genomes]
rs1675764	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1675765	0.84[ASN][1000 genomes]
rs1675767	0.84[ASN][1000 genomes]
rs1675769	0.84[ASN][1000 genomes]
rs1675772	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs1675781	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1675785	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1675787	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1675789	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1675790	0.84[ASN][1000 genomes]
rs1731423	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1731427	0.90[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1731429	0.83[ASN][1000 genomes]
rs1731430	0.84[ASN][1000 genomes]
rs1731431	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs1731432	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs1731434	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1731452	0.84[ASN][1000 genomes]
rs1731454	0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1731456	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1731457	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1731458	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1731459	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2219629	0.84[ASN][1000 genomes]
rs2407783	0.84[ASN][1000 genomes]
rs2447113	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2614394	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2951435	0.87[ASN][1000 genomes]
rs3764004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4238089	0.84[ASN][1000 genomes]
rs4238090	0.84[ASN][1000 genomes]
rs4238091	0.84[ASN][1000 genomes]
rs4354753	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4363674	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4469953	0.84[ASN][1000 genomes]
rs4537822	0.84[ASN][1000 genomes]
rs4572198	0.84[ASN][1000 genomes]
rs4572199	0.84[ASN][1000 genomes]
rs4609659	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4768053	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs4768538	0.84[ASN][1000 genomes]
rs5019975	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6582484	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7295151	0.84[ASN][1000 genomes]
rs7305609	0.84[ASN][1000 genomes]
rs73096934	0.84[ASN][1000 genomes]
rs7955615	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899048	chr12:44209423-44307888	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7972025	DBX2	cis	cerebellum	SCAN
rs7972025	PUS7L	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44208400-44223600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:44220400-44223000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:44221800-44225000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:44222000-44224200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:44222200-44224200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links