Variant report

Variant	rs7574345
Chromosome Location	chr2:180635236-180635237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180628206..180630948-chr2:180635078..180637285,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1139	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12052744	0.86[ASN][1000 genomes]
rs12052765	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12053119	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12465379	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12466207	0.92[ASN][1000 genomes]
rs12472888	0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs12473571	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1385972	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1462208	0.81[CEU][hapmap]
rs1533384	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs16866963	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs16866968	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs16866978	0.81[ASN][1000 genomes]
rs16866986	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16866987	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16866989	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16866991	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs16866992	0.81[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs28404240	0.95[ASN][1000 genomes]
rs356407	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356413	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55728092	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58217303	0.82[ASN][1000 genomes]
rs7592797	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7607561	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[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	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428731	chr2:180629389-180805171	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7574345	ITGA4	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180633800-180637200	Weak transcription	Fetal Lung	lung
2	chr2:180634400-180638400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:180634400-180638800	Weak transcription	Liver	Liver
4	chr2:180634600-180644000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:180635000-180635800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:180635000-180643000	Weak transcription	Right Atrium	heart
7	chr2:180635200-180636200	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links