Variant report

Variant	rs6662859
Chromosome Location	chr1:179398536-179398537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1060775	0.87[ASW][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs10753193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10798672	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10798678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798682	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10913763	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913776	0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10913794	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10913804	1.00[JPT][hapmap]
rs10913807	0.85[GIH][hapmap];1.00[JPT][hapmap]
rs12122753	0.90[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12131398	1.00[JPT][hapmap]
rs12131400	1.00[JPT][hapmap]
rs12136100	1.00[JPT][hapmap]
rs12140800	0.82[CHD][hapmap]
rs1328596	1.00[JPT][hapmap]
rs1410590	0.87[ASW][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs1831180	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1928004	0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2026014	1.00[JPT][hapmap]
rs2152319	0.83[CHD][hapmap]
rs3753525	0.83[CHD][hapmap]
rs3753527	0.83[CHD][hapmap]
rs3898486	0.82[GIH][hapmap]
rs4255343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4297245	0.82[GIH][hapmap]
rs4360482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4421551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4584358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4606280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap]
rs4625242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4652386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4652404	1.00[JPT][hapmap]
rs6425558	0.92[GIH][hapmap]
rs6659294	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6683623	0.92[GIH][hapmap]
rs6696896	0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap]
rs6697280	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6697285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697373	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6698201	1.00[JPT][hapmap]
rs749960	1.00[JPT][hapmap]
rs7512551	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs7514278	0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap]
rs7517766	1.00[JPT][hapmap]
rs7518843	0.82[EUR][1000 genomes]
rs7522064	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7529133	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7535603	0.89[CEU][hapmap];0.90[YRI][hapmap]
rs7540732	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7542099	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs928016	0.87[ASW][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs963062	1.00[JPT][hapmap]
rs964982	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs9787088	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3514400	chr1:179349344-179400533	Enhancers Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3514401	chr1:179349344-179400533	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3451112	chr1:179352344-179400533	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv1819329	chr1:179371973-179442337	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv466217	chr1:179371973-179477921	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv548297	chr1:179371973-179477921	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv548298	chr1:179376896-179436288	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6662859	TDRD5	cis	parietal	SCAN
rs6662859	SNORD80	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179398400-179398800	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links