Variant report

Variant	rs2877560
Chromosome Location	chr3:121699238-121699239
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121698386..121699300-chr3:121714459..121714981,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10934565	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488334	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488851	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491991	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493408	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496036	0.82[AMR][1000 genomes]
rs12496318	0.88[GIH][hapmap]
rs12497349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12498028	0.85[EUR][1000 genomes]
rs12629742	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12630486	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632345	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12637351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637968	0.84[EUR][1000 genomes]
rs12638492	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13067270	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13083557	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089878	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13093171	0.81[EUR][1000 genomes]
rs1344279	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1523519	0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs1920290	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920291	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920297	0.83[EUR][1000 genomes]
rs1920298	0.92[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs1920299	0.92[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs1920309	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1986712	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2091664	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293611	0.82[AMR][1000 genomes]
rs2332033	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2332035	0.82[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2689285	0.84[EUR][1000 genomes]
rs2689290	0.88[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2877561	1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34158925	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181646	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34478505	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34543553	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34566912	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34696871	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34837785	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35101693	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35415993	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35737776	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35902163	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3915060	0.90[EUR][1000 genomes]
rs3942629	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4118376	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4285028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4305455	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4676758	0.82[EUR][1000 genomes]
rs6790281	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71329246	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71329247	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71329249	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73855465	0.84[EUR][1000 genomes]
rs73855476	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73855480	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855481	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615571	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623901	0.88[GIH][hapmap]
rs7637495	0.92[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs7640872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651226	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2877560	SLC15A2	cis	cerebellum	SCAN
rs2877560	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs2877560	IQCB1	cis	parietal	SCAN
rs2877560	HEG1	cis	cerebellum	SCAN
rs2877560	IQCB1	cis	Esophagus Muscularis	GTEx
rs2877560	EAF2	cis	lymphoblastoid	seeQTL
rs2877560	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs2877560	IQCB1	cis	cerebellum	SCAN
rs2877560	ILDR1	Cis_1M	lymphoblastoid	RTeQTL
rs2877560	EAF2	cis	cerebellum	SCAN
rs2877560	EAF2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121698200-121699600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:121698200-121699600	Enhancers	Fetal Intestine Small	intestine
3	chr3:121698200-121699600	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr3:121698400-121699400	Flanking Active TSS	HMEC	breast
5	chr3:121698400-121699600	Enhancers	Fetal Intestine Large	intestine
6	chr3:121698400-121702000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:121698400-121704800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:121698600-121699400	Enhancers	Primary B cells from cord blood	blood
9	chr3:121698600-121700000	Enhancers	Stomach Mucosa	stomach
10	chr3:121699000-121699400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:121699000-121704800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:121699000-121711200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:121699200-121699600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:121699200-121699800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:121699200-121700000	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links