Variant report

Variant	rs2312462
Chromosome Location	chr3:49601255-49601256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49599253..49602377-chr3:49606582..49609679,3	K562	blood:
2	chr3:49598309..49602377-chr3:49605664..49611011,5	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 37 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10155014	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10452032	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap]
rs1078341	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs10865956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.98[EUR][1000 genomes]
rs1106620	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130204	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130207	0.93[AFR][1000 genomes]
rs11130208	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs11130211	0.80[YRI][hapmap]
rs11130217	0.82[ASW][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs11709734	1.00[CHD][hapmap]
rs11719762	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11720705	1.00[CHD][hapmap]
rs11928090	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.99[EUR][1000 genomes]
rs12637313	1.00[CHD][hapmap];0.95[YRI][hapmap]
rs12715437	0.82[ASW][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs13096474	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096480	0.93[YRI][hapmap]
rs13322887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1352889	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs1464569	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	0.82[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs1532204	0.97[AFR][1000 genomes]
rs1586827	0.95[YRI][hapmap]
rs1982861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029591	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs2131108	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs2140270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs2177268	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs2329021	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs2329025	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	0.86[YRI][hapmap]
rs34890793	1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap]
rs3866330	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870339	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870341	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905330	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241405	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs4241407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855833	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs4855837	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4855838	0.84[AFR][1000 genomes]
rs4855845	0.95[YRI][hapmap]
rs4855846	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs4855853	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4855858	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855869	0.85[EUR][1000 genomes]
rs4855882	1.00[CHD][hapmap]
rs4855885	1.00[CHD][hapmap]
rs56049603	0.83[EUR][1000 genomes]
rs56127630	0.82[EUR][1000 genomes]
rs56324858	0.81[EUR][1000 genomes]
rs57273516	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259933	0.86[EUR][1000 genomes]
rs62259943	0.80[EUR][1000 genomes]
rs62259947	0.82[EUR][1000 genomes]
rs62261183	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62261249	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446275	0.86[EUR][1000 genomes]
rs6446284	0.87[AFR][1000 genomes]
rs6446285	1.00[CHD][hapmap]
rs6769744	1.00[ASN][1000 genomes]
rs6774202	1.00[CHD][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap]
rs6783003	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6785045	0.82[EUR][1000 genomes]
rs6797299	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs6805609	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs72934271	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73088137	0.83[EUR][1000 genomes]
rs7355800	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7374731	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7613491	0.90[EUR][1000 genomes]
rs7619789	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620024	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622786	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7625857	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7628207	1.00[CHD][hapmap]
rs7644148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7647973	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7648995	0.82[EUR][1000 genomes]
rs7651372	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7653505	1.00[CHD][hapmap];0.84[MKK][hapmap]
rs8897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs940045	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654010	0.84[EUR][1000 genomes]
rs974495	1.00[ASN][1000 genomes]
rs9757181	1.00[CEU][hapmap]
rs9809237	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9817807	0.80[EUR][1000 genomes]
rs9824435	1.00[CHD][hapmap]
rs9835157	0.82[ASW][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs9842132	0.80[EUR][1000 genomes]
rs9849038	1.00[CHD][hapmap]
rs9860055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9861027	0.82[EUR][1000 genomes]
rs9862534	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870858	1.00[CHD][hapmap]
rs9871024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9883000	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:37)

SNP	Gene	Cis/trans	Tissue	Source
rs2312462	AMT	cis	Adipose Subcutaneous	GTEx
rs2312462	GMPPB	cis	parietal	SCAN
rs2312462	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs2312462	LZTFL1	cis	cerebellum	SCAN
rs2312462	P4HTM	cis	parietal	SCAN
rs2312462	WDR6	cis	Esophagus Muscularis	GTEx
rs2312462	DALRD3	cis	cerebellum	SCAN
rs2312462	AMT	cis	Artery Aorta	GTEx
rs2312462	AMT	cis	lymphoblastoid	seeQTL
rs2312462	WDR6	cis	cerebellum	SCAN
rs2312462	AMT	cis	cerebellum	SCAN
rs2312462	NICN1	cis	Thyroid	GTEx
rs2312462	ZNF589	cis	parietal	SCAN
rs2312462	AMT	cis	parietal	SCAN
rs2312462	NME6	cis	cerebellum	SCAN
rs2312462	NICN1	cis	cerebellum	SCAN
rs2312462	AMT	cis	Artery Tibial	GTEx
rs2312462	GNL3	cis	cerebellum	SCAN
rs2312462	NICN1-AS1	cis	Thyroid	GTEx
rs2312462	WDR6	cis	Muscle Skeletal	GTEx
rs2312462	DALRD3	cis	parietal	SCAN
rs2312462	WDR6	cis	Nerve Tibial	GTEx
rs2312462	NCKIPSD	cis	multi-tissue	Pritchard
rs2312462	AMT	cis	Thyroid	GTEx
rs2312462	AMT	cis	Esophagus Mucosa	GTEx
rs2312462	SEMA3G	cis	cerebellum	SCAN
rs2312462	WDR6	cis	parietal	SCAN
rs2312462	AMT	cis	multi-tissue	Pritchard
rs2312462	NICN1	cis	multi-tissue	Pritchard
rs2312462	AMT	cis	Esophagus Muscularis	GTEx
rs2312462	AMT	cis	Whole Blood	GTEx
rs2312462	AMT	cis	Nerve Tibial	GTEx
rs2312462	AMT	cis	Muscle Skeletal	GTEx
rs2312462	GPX1	cis	parietal	SCAN
rs2312462	WDR6	cis	multi-tissue	Pritchard
rs2312462	AMT	cis	lung	GTEx
rs2312462	QRICH1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49596000-49615000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:49596000-49616800	Weak transcription	Fetal Brain Female	brain
3	chr3:49598000-49602000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:49598200-49601600	Weak transcription	Brain Angular Gyrus	brain
5	chr3:49598800-49603000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:49600000-49604800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:49600000-49607800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:49601000-49601600	Enhancers	Stomach Mucosa	stomach
9	chr3:49601200-49606000	Weak transcription	HepG2	liver
10	chr3:49601200-49612200	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links