Variant report

Variant	rs902711
Chromosome Location	chr3:70032376-70032377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1021413	0.91[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11718882	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923682	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11926368	0.84[ASN][1000 genomes]
rs12495230	0.84[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12639523	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1491687	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1491688	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1491689	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1491695	0.89[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs1491698	1.00[CHB][hapmap];0.94[YRI][hapmap];0.84[ASN][1000 genomes]
rs1546075	0.85[ASN][1000 genomes]
rs17727959	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1844877	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1873583	0.84[ASN][1000 genomes]
rs1873584	0.84[ASN][1000 genomes]
rs1907646	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1907647	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2131026	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172211	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28524674	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2874270	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34790356	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35180789	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35416604	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35996477	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36125122	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772111	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821364	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3967688	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4635708	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4855331	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855453	0.91[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855454	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855455	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855456	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55842620	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56351003	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576	0.91[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6549254	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6549255	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6549256	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6549257	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6549258	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6549259	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6549260	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6549261	1.00[CHB][hapmap];0.87[LWK][hapmap];0.94[YRI][hapmap];0.85[ASN][1000 genomes]
rs6549262	0.85[ASN][1000 genomes]
rs6549264	0.84[ASN][1000 genomes]
rs6549265	0.84[ASN][1000 genomes]
rs6771970	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6772684	0.84[ASN][1000 genomes]
rs6784666	0.85[ASN][1000 genomes]
rs6809508	0.84[ASN][1000 genomes]
rs704246	0.87[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73119519	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7429562	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7431913	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs902712	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923702	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9310178	1.00[CHB][hapmap];0.94[YRI][hapmap];0.84[ASN][1000 genomes]
rs9310179	1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[LWK][hapmap];0.94[YRI][hapmap];0.85[ASN][1000 genomes]
rs9310180	0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs956436	0.84[ASN][1000 genomes]
rs9815287	0.86[ASN][1000 genomes]
rs9834141	0.86[ASN][1000 genomes]
rs9839734	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9840397	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9840590	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9849031	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9851891	0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9863457	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9868203	0.84[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	nsv533396	chr3:69964029-70538306	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs902711	GXYLT2	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:70030000-70036800	Weak transcription	Brain Hippocampus Middle	brain
2	chr3:70031600-70032600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:70031800-70032600	Enhancers	Liver	Liver
4	chr3:70031800-70033400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:70031800-70033400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:70031800-70033600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:70032000-70032600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:70032000-70033400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
9	chr3:70032200-70032400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr3:70032200-70033200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:70032200-70033400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr3:70032200-70033600	Enhancers	Monocytes-CD14+_RO01746	blood

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