Variant report

Variant	rs6794475
Chromosome Location	chr3:46160178-46160179
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1072755	0.84[CEU][hapmap]
rs11130080	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11130085	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130086	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1118879	0.91[ASN][1000 genomes]
rs11917890	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11929281	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12485978	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12495073	0.84[CEU][hapmap]
rs12496322	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12629632	0.91[ASN][1000 genomes]
rs12630101	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs12635657	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs12637023	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12639598	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs13059919	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13060901	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs13065737	0.91[ASN][1000 genomes]
rs13066048	0.84[CEU][hapmap]
rs13073861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077099	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13077923	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13078053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13082280	0.89[ASN][1000 genomes]
rs13434029	0.89[ASN][1000 genomes]
rs13434336	0.86[ASN][1000 genomes]
rs1392290	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs1491959	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.86[ASN][1000 genomes]
rs1500005	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1546077	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.90[ASN][1000 genomes]
rs1546078	0.90[ASN][1000 genomes]
rs1546079	0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1552489	0.84[CEU][hapmap]
rs1602579	0.91[ASN][1000 genomes]
rs1604069	0.85[ASN][1000 genomes]
rs17078577	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1909595	0.83[ASN][1000 genomes]
rs1909596	0.85[ASN][1000 genomes]
rs1976366	0.90[ASN][1000 genomes]
rs1976367	0.90[ASN][1000 genomes]
rs1994490	0.86[JPT][hapmap]
rs2036292	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2054866	0.84[CEU][hapmap]
rs2131091	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[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];0.98[ASN][1000 genomes]
rs2220678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2248228	0.92[CEU][hapmap]
rs2373150	0.89[ASN][1000 genomes]
rs2373151	0.89[ASN][1000 genomes]
rs2373153	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373154	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.91[ASN][1000 genomes]
rs34067839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34381514	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35359253	0.91[ASN][1000 genomes]
rs35462017	0.91[ASN][1000 genomes]
rs35567508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36111470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3733100	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs3774634	0.84[CEU][hapmap]
rs3774639	0.84[CEU][hapmap]
rs3796375	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs3821884	0.86[JPT][hapmap]
rs3851347	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4318588	0.89[ASN][1000 genomes]
rs4333119	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4535265	0.84[CEU][hapmap]
rs4682806	0.87[ASN][1000 genomes]
rs4682809	0.90[ASN][1000 genomes]
rs4682810	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4683157	0.84[CEU][hapmap]
rs4683175	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683176	0.81[EUR][1000 genomes]
rs4683178	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56307311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59521415	0.91[ASN][1000 genomes]
rs61079448	0.91[ASN][1000 genomes]
rs6441944	0.91[ASN][1000 genomes]
rs6764042	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs6776028	0.87[ASN][1000 genomes]
rs6780163	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs6784214	0.90[ASN][1000 genomes]
rs6794103	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6795629	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6800484	0.87[ASN][1000 genomes]
rs6809381	0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs730983	0.88[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs737452	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap]
rs751552	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs751553	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs7610518	0.91[ASN][1000 genomes]
rs7616464	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7623460	0.85[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs7631598	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7643426	0.81[CHB][hapmap]
rs9311386	0.85[ASN][1000 genomes]
rs9311387	0.85[ASN][1000 genomes]
rs936938	0.84[CEU][hapmap]
rs9637425	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9824886	0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs9870445	0.85[ASN][1000 genomes]
rs9876587	0.85[ASN][1000 genomes]
rs9990063	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6794475	UBA7	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46146800-46164400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:46148400-46160200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:46152600-46165200	Weak transcription	Spleen	Spleen
4	chr3:46152800-46162400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:46156800-46168000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:46157200-46166600	Weak transcription	Psoas Muscle	Psoas
7	chr3:46157200-46168600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:46158000-46163200	Weak transcription	Fetal Stomach	stomach
9	chr3:46158200-46162400	Weak transcription	NHDF-Ad	bronchial
10	chr3:46158200-46162800	Weak transcription	Fetal Lung	lung
11	chr3:46158600-46160800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:46158800-46160800	Weak transcription	HMEC	breast
13	chr3:46158800-46162400	Weak transcription	NHEK	skin
14	chr3:46158800-46162600	Weak transcription	Hela-S3	cervix
15	chr3:46158800-46162600	Weak transcription	NHLF	lung
16	chr3:46159400-46161400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:46159600-46165000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:46159600-46165000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:46159600-46165000	Weak transcription	Adipose Nuclei	Adipose
20	chr3:46159800-46160800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:46159800-46161600	Weak transcription	Placenta	Placenta
22	chr3:46159800-46164400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:46159800-46165000	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links