Variant report

Variant	rs675353
Chromosome Location	chr5:112810088-112810089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112809363..112813589-chr5:112821986..112825015,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10071966	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1035408	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1132528	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap]
rs12659978	0.96[CEU][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13190054	0.86[CHB][hapmap]
rs1517208	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1517210	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs154039	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs154040	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1593953	0.90[AMR][1000 genomes]
rs164251	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs164253	0.91[AMR][1000 genomes]
rs171181	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17327526	0.83[LWK][hapmap]
rs173903	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1820056	0.96[CEU][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs182987	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1838207	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1845290	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs190453	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2303717	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs2416282	0.84[ASW][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2431548	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2434664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2434665	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs255856	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs255858	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs255863	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs255867	0.82[EUR][1000 genomes]
rs255874	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs26960	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs26983	0.83[AMR][1000 genomes]
rs26985	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs26987	0.89[ASN][1000 genomes]
rs26988	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs27566	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs27700	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2910018	0.96[CEU][hapmap];0.88[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2914252	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs34075952	0.84[AMR][1000 genomes]
rs348927	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348933	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs348936	0.83[AMR][1000 genomes]
rs348949	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs348950	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs348953	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs348959	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs36612	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs368352	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3763139	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs3857435	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3857437	0.85[AMR][1000 genomes]
rs3906371	0.96[MEX][hapmap];0.83[AMR][1000 genomes]
rs3936062	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs406288	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs423089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4235796	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4398627	0.87[CHB][hapmap];0.84[MEX][hapmap]
rs4415069	0.96[CEU][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4438867	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4444963	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs459428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs461034	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs463216	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4639215	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs465898	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs466564	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4705830	0.96[CEU][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705831	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs485210	0.84[ASW][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap]
rs492346	0.84[ASW][hapmap];0.88[MEX][hapmap]
rs57617774	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62373764	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6594711	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6594736	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6869097	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs6881976	0.92[CEU][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7702120	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7702405	0.81[EUR][1000 genomes]
rs7703233	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7708084	0.81[CHB][hapmap]
rs7713348	0.84[AMR][1000 genomes]
rs7713378	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7722276	0.86[ASW][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap]
rs7727449	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs7730802	0.85[AMR][1000 genomes]
rs9326895	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9552	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap]
rs9686772	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs675353	LILRP2	trans	parietal	SCAN
rs675353	YTHDC2	cis	cerebellum	SCAN
rs675353	YTHDC2	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112807800-112821600	Weak transcription	HMEC	breast
2	chr5:112808200-112810200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:112808800-112812400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:112809600-112810600	Enhancers	Fetal Heart	heart
5	chr5:112809600-112810600	Enhancers	K562	blood
6	chr5:112809800-112810200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr5:112809800-112810200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:112809800-112810400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:112810000-112810200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:112810000-112810200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:112810000-112810200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr5:112810000-112810400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:112810000-112810400	Enhancers	NHEK	skin
14	chr5:112810000-112810600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:112810000-112811000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links