Variant report

Variant	rs9858335
Chromosome Location	chr3:160760146-160760147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160739787..160741430-chr3:160758858..160761533,2	MCF-7	breast:
2	chr3:160748960..160749535-chr3:160759816..160760384,2	MCF-7	breast:
3	chr3:160759280..160760955-chr3:160782590..160785077,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10433352	0.83[CHD][hapmap]
rs10513560	0.97[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs10936216	0.85[AMR][1000 genomes]
rs12496196	0.86[JPT][hapmap]
rs12690576	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs13325518	0.87[CHD][hapmap]
rs1374787	0.95[CEU][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs1447609	0.82[AMR][1000 genomes]
rs1447626	0.91[CEU][hapmap]
rs1530636	0.83[CEU][hapmap];0.97[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs1562465	0.82[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs1562466	0.89[CHD][hapmap]
rs1580253	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1580254	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16831796	0.83[CHD][hapmap]
rs1868108	0.95[CEU][hapmap]
rs1868109	0.95[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs2061580	0.84[CHD][hapmap]
rs2121721	0.80[TSI][hapmap]
rs2376476	0.89[EUR][1000 genomes]
rs2376477	0.90[EUR][1000 genomes]
rs2889391	0.85[AMR][1000 genomes]
rs34462546	0.80[AMR][1000 genomes]
rs34884182	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35187206	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4679928	0.89[EUR][1000 genomes]
rs6441345	0.95[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes]
rs6441346	0.85[AMR][1000 genomes]
rs6763532	0.85[JPT][hapmap];0.85[AMR][1000 genomes]
rs6769927	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6770180	0.85[AMR][1000 genomes]
rs6774203	0.95[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs6787694	0.87[CHD][hapmap]
rs6791375	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6808311	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs733948	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs7611005	0.88[EUR][1000 genomes]
rs7628389	0.85[CHD][hapmap]
rs778650	0.87[CHD][hapmap]
rs778651	0.80[JPT][hapmap]
rs796610	0.84[CHD][hapmap]
rs898677	0.85[CHD][hapmap]
rs898682	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs956447	0.95[CEU][hapmap]
rs964533	0.81[CHB][hapmap]
rs9812507	0.81[CHB][hapmap]
rs9818081	0.84[CHD][hapmap]
rs9832109	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs9839984	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9840600	0.80[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9846254	0.84[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9857743	0.82[CEU][hapmap]
rs9860182	0.84[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9873705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9881807	0.95[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9858335	PPM1L	cis	cerebellum	SCAN
rs9858335	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs9858335	C3orf57	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160745200-160782600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:160753800-160763200	Weak transcription	Primary T cells from cord blood	blood
3	chr3:160759000-160760800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:160759200-160760600	Enhancers	HepG2	liver
5	chr3:160759600-160760400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:160759600-160760600	Enhancers	Liver	Liver
7	chr3:160759600-160761800	Enhancers	Osteobl	bone
8	chr3:160759800-160760200	Flanking Active TSS	Fetal Kidney	kidney
9	chr3:160759800-160760400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:160759800-160760400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:160759800-160760400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:160759800-160760400	Enhancers	Pancreas	Pancrea
13	chr3:160759800-160760400	Enhancers	Stomach Smooth Muscle	stomach
14	chr3:160760000-160760200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:160760000-160760400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:160760000-160760400	Enhancers	GM12878-XiMat	blood
17	chr3:160760000-160760400	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links