Variant report

Variant	rs9948889
Chromosome Location	chr18:11777968-11777969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:11775931..11778532-chr18:11780159..11782113,2	MCF-7	breast:
2	chr18:11776601..11778120-chr18:11779669..11782616,2	K562	blood:
3	chr18:11775863..11778120-chr18:11779319..11781169,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10468681	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs11080534	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs11872939	0.85[LWK][hapmap]
rs12326439	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12327266	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12965108	0.83[CHD][hapmap]
rs12965256	0.83[CHD][hapmap]
rs1364632	0.83[CHD][hapmap]
rs1477481	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs1477483	0.99[ASN][1000 genomes]
rs1477484	0.83[LWK][hapmap]
rs1786568	0.91[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1941224	0.99[ASN][1000 genomes]
rs2161960	0.98[ASN][1000 genomes]
rs2161961	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs28651978	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4797579	0.94[ASN][1000 genomes]
rs57536188	0.88[ASN][1000 genomes]
rs59700035	0.84[ASN][1000 genomes]
rs60736251	0.82[ASN][1000 genomes]
rs7226993	0.84[ASN][1000 genomes]
rs8084246	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8084992	0.97[ASN][1000 genomes]
rs8086766	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8094039	0.95[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs8098539	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs8099153	0.85[LWK][hapmap]
rs9303746	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9303748	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs9303749	0.83[CHD][hapmap]
rs9675368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9676126	0.97[ASN][1000 genomes]
rs9962277	0.86[CHB][hapmap];0.88[CHD][hapmap]

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	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833590	chr18:11757329-11924539	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9948889	PPP4R1	cis	cerebellum	SCAN
rs9948889	TWSG1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11758400-11785600	Weak transcription	Brain Anterior Caudate	brain
2	chr18:11763400-11780400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr18:11767600-11785400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr18:11767600-11789000	Weak transcription	Esophagus	oesophagus
5	chr18:11767800-11783800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr18:11767800-11784000	Weak transcription	Aorta	Aorta
7	chr18:11771800-11783800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr18:11772400-11780600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr18:11773400-11784600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr18:11777800-11778800	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links