Variant report

Variant	rs790827
Chromosome Location	chr5:127075777-127075778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTXN3-1	chr5:127075535-127075979	ENSG00000230561

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10041967	0.89[EUR][1000 genomes]
rs10061252	0.89[EUR][1000 genomes]
rs1007623	0.89[EUR][1000 genomes]
rs10519953	1.00[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10519960	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1086523	0.88[EUR][1000 genomes]
rs1086524	0.86[EUR][1000 genomes]
rs1086525	0.88[EUR][1000 genomes]
rs1086526	0.88[EUR][1000 genomes]
rs1086527	0.91[EUR][1000 genomes]
rs1086529	0.88[EUR][1000 genomes]
rs1086530	0.87[EUR][1000 genomes]
rs1086531	0.91[EUR][1000 genomes]
rs1086532	0.91[EUR][1000 genomes]
rs1086533	0.88[EUR][1000 genomes]
rs1086534	0.89[EUR][1000 genomes]
rs1088167	0.88[EUR][1000 genomes]
rs10900792	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1092720	0.88[EUR][1000 genomes]
rs11241938	0.91[EUR][1000 genomes]
rs11241939	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11241942	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11950864	0.95[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11957799	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1213827	0.89[EUR][1000 genomes]
rs1228156	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1234542	0.89[EUR][1000 genomes]
rs12652197	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12653785	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1399829	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1421747	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1432958	0.91[EUR][1000 genomes]
rs1515640	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1560673	0.95[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs173580	0.89[EUR][1000 genomes]
rs173581	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs173582	0.88[EUR][1000 genomes]
rs1816404	0.89[EUR][1000 genomes]
rs1816405	0.89[EUR][1000 genomes]
rs1849938	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs187461	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1897525	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs193736	0.91[EUR][1000 genomes]
rs248689	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs248690	0.86[EUR][1000 genomes]
rs248691	0.83[EUR][1000 genomes]
rs248692	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs248696	0.87[EUR][1000 genomes]
rs248698	0.87[EUR][1000 genomes]
rs248700	0.85[EUR][1000 genomes]
rs248701	0.86[EUR][1000 genomes]
rs248702	0.86[EUR][1000 genomes]
rs248706	0.86[EUR][1000 genomes]
rs248709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs248711	0.91[EUR][1000 genomes]
rs248712	0.88[EUR][1000 genomes]
rs248713	0.91[EUR][1000 genomes]
rs248715	0.88[EUR][1000 genomes]
rs248716	0.92[EUR][1000 genomes]
rs248717	0.91[EUR][1000 genomes]
rs248718	0.89[EUR][1000 genomes]
rs248720	0.88[EUR][1000 genomes]
rs248721	0.88[EUR][1000 genomes]
rs248722	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248724	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248730	0.91[EUR][1000 genomes]
rs248731	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs248732	0.91[EUR][1000 genomes]
rs248733	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs248735	0.91[EUR][1000 genomes]
rs248737	0.90[EUR][1000 genomes]
rs248738	0.91[EUR][1000 genomes]
rs248739	0.91[EUR][1000 genomes]
rs248740	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs248741	0.91[EUR][1000 genomes]
rs248742	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2569142	0.91[EUR][1000 genomes]
rs2569144	0.91[EUR][1000 genomes]
rs2569146	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2569148	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2673749	0.90[EUR][1000 genomes]
rs2673750	0.88[EUR][1000 genomes]
rs2673763	0.91[EUR][1000 genomes]
rs2673764	0.84[EUR][1000 genomes]
rs2673772	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4340958	0.86[EUR][1000 genomes]
rs4361571	0.89[EUR][1000 genomes]
rs45074	0.86[EUR][1000 genomes]
rs54201	0.91[EUR][1000 genomes]
rs57883466	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59513079	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62373501	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62373502	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6595789	0.92[EUR][1000 genomes]
rs7714847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs7736233	0.84[EUR][1000 genomes]
rs791071	0.88[EUR][1000 genomes]
rs791072	0.88[EUR][1000 genomes]
rs791073	0.88[EUR][1000 genomes]
rs791074	0.91[EUR][1000 genomes]
rs809349	0.88[EUR][1000 genomes]
rs812059	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs899190	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830480	chr5:126964751-127124522	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs790827	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127075000-127075800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:127075200-127075800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:127075200-127075800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:127075200-127075800	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr5:127075200-127076000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr5:127075200-127076000	Enhancers	Fetal Thymus	thymus
7	chr5:127075200-127076200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:127075200-127076200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:127075200-127076200	Active TSS	K562	blood
10	chr5:127075600-127075800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr5:127075600-127075800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr5:127075600-127075800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr5:127075600-127075800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:127075600-127076000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
15	chr5:127075600-127076000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr5:127075600-127076000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell

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