Variant report

Variant	rs2724691
Chromosome Location	chr3:137850003-137850004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1564496	0.83[EUR][1000 genomes]
rs1600697	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2170309	0.86[CEU][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2219936	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246945	0.86[CEU][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2251550	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2346744	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346745	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346747	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622694	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622695	0.86[CEU][hapmap];0.89[CHD][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2622696	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622697	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622699	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622700	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs2622714	0.84[JPT][hapmap]
rs2622732	0.80[EUR][1000 genomes]
rs2622733	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2622734	0.95[CEU][hapmap];0.84[CHB][hapmap]
rs2622735	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2622736	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622737	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622739	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622740	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622742	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622743	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622744	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724687	0.82[CEU][hapmap]
rs2724690	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2724692	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724710	0.82[ASN][1000 genomes]
rs2724711	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724712	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2724725	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2724726	0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2724727	0.95[CEU][hapmap];0.85[CHB][hapmap];0.80[EUR][1000 genomes]
rs3732839	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs405602	0.80[JPT][hapmap]
rs608594	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs7430414	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7613041	0.80[EUR][1000 genomes]
rs7613558	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7632402	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774803	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs774807	0.95[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs774808	0.95[CEU][hapmap];0.80[CHB][hapmap]
rs774810	0.95[CEU][hapmap]
rs774813	0.95[CEU][hapmap];0.80[CHB][hapmap]
rs774814	0.95[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs811811	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs9827617	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9840008	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9851548	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2724691	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx
rs2724691	A4GNT	cis	lung	GTEx
rs2724691	A4GNT	cis	Nerve Tibial	GTEx
rs2724691	DBR1	Cis_1M	lymphoblastoid	RTeQTL
rs2724691	A4GNT	cis	Adipose Subcutaneous	GTEx
rs2724691	A4GNT	cis	Artery Tibial	GTEx
rs2724691	A4GNT	cis	Thyroid	GTEx
rs2724691	DBR1	cis	normal skin	skin_eQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137843800-137851800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:137844800-137851000	Weak transcription	Stomach Mucosa	stomach
3	chr3:137845000-137851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:137845200-137853200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:137847800-137851200	Active TSS	Fetal Stomach	stomach
6	chr3:137849800-137850200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:137850000-137851800	Weak transcription	Pancreas	Pancrea

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