Variant report

Variant	rs11928090
Chromosome Location	chr3:49604904-49604905
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	chr3:49603222..49606574-chr3:49608966..49612068,4	K562	blood:
2	chr3:49603620..49605380-chr3:49707989..49710873,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10155014	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1106620	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130204	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130211	1.00[CHB][hapmap]
rs11719762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12583	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13096474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1352889	1.00[CHB][hapmap]
rs1464569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	1.00[CHB][hapmap]
rs1982861	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2177268	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2312462	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329025	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34890793	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs3866330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870339	0.95[CEU][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870341	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052546	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855833	1.00[CHB][hapmap]
rs4855837	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4855853	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4855858	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855869	0.85[EUR][1000 genomes]
rs56049603	0.83[EUR][1000 genomes]
rs56127630	0.82[EUR][1000 genomes]
rs56324858	0.81[EUR][1000 genomes]
rs57273516	0.82[AFR][1000 genomes];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	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62261249	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446275	0.86[EUR][1000 genomes]
rs6769744	1.00[ASN][1000 genomes]
rs6774202	1.00[CHB][hapmap]
rs6783003	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6785045	0.82[EUR][1000 genomes]
rs6805609	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs72934271	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73088137	0.83[EUR][1000 genomes]
rs7355800	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7374731	0.85[AFR][1000 genomes];0.91[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	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7625857	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7644148	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7647973	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7648995	0.82[EUR][1000 genomes]
rs7651372	0.90[EUR][1000 genomes]
rs7653505	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs8897	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs940045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][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	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9817807	0.80[EUR][1000 genomes]
rs9842132	0.80[EUR][1000 genomes]
rs9860055	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9861027	0.82[EUR][1000 genomes]
rs9862534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871024	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[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	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs11928090	WDR6	cis	Nerve Tibial	GTEx
rs11928090	AMT	cis	Adipose Subcutaneous	GTEx
rs11928090	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs11928090	WDR6	cis	Esophagus Muscularis	GTEx
rs11928090	AMT	cis	Esophagus Mucosa	GTEx
rs11928090	AMT	cis	Esophagus Muscularis	GTEx
rs11928090	AMT	cis	Whole Blood	GTEx
rs11928090	WDR6	cis	lung	GTEx
rs11928090	AMT	cis	Artery Tibial	GTEx
rs11928090	AMT	cis	Muscle Skeletal	GTEx
rs11928090	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs11928090	NICN1	cis	Thyroid	GTEx
rs11928090	AMT	cis	Artery Aorta	GTEx
rs11928090	AMT	cis	lung	GTEx
rs11928090	WDR6	cis	Muscle Skeletal	GTEx
rs11928090	AMT	cis	Nerve Tibial	GTEx
rs11928090	NICN1-AS1	cis	Thyroid	GTEx
rs11928090	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs11928090	AMT	cis	Thyroid	GTEx

Chromatin state (count:14 , 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	chr3:49600000-49607800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:49601200-49606000	Weak transcription	HepG2	liver
5	chr3:49601200-49612200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:49602000-49606400	Weak transcription	Brain Angular Gyrus	brain
7	chr3:49602400-49607200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:49604400-49605200	Enhancers	HMEC	breast
9	chr3:49604600-49605400	Enhancers	NHEK	skin
10	chr3:49604800-49605000	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr3:49604800-49605200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:49604800-49605200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:49604800-49605200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:49604800-49605600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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