Variant report

Variant	rs13429968
Chromosome Location	chr2:85797665-85797666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85774272..85776282-chr2:85797385..85799189,3	K562	blood:
2	chr2:85792131..85794386-chr2:85795797..85798233,4	K562	blood:
3	chr2:85788623..85792112-chr2:85794974..85798818,4	K562	blood:
4	chr2:85797057..85798871-chr2:85803287..85805512,2	K562	blood:
5	chr2:85787083..85789118-chr2:85797311..85798959,3	MCF-7	breast:
6	chr2:85765001..85768151-chr2:85794146..85798905,4	K562	blood:
7	chr2:85554962..85556625-chr2:85795107..85797977,2	MCF-7	breast:
8	chr2:85797355..85800096-chr2:85833423..85836013,2	K562	blood:
9	chr2:85792880..85794386-chr2:85796161..85797994,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VAMP5-1	chr2:85796667-85797685	l_1875_chr2:85792256-85797685_thyroid

No data

Variant related genes	Relation type
ENSG00000115486	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000152291	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10166612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[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]
rs10167018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10172793	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10174551	0.84[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10179904	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10187218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190585	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10196357	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198001	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10198761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10496316	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12714142	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12714143	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12714144	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714146	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714147	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12994163	0.84[CEU][hapmap]
rs13000511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387999	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13394092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13406611	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13406935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13408713	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13409377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13425821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[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]
rs13431159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13431962	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13432584	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17430670	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];1.00[ASN][1000 genomes]
rs17508727	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];1.00[ASN][1000 genomes]
rs17508809	1.00[CHB][hapmap]
rs17735885	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2121397	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[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]
rs28398892	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28479378	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28564788	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28800839	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28810460	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34212016	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34214220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34565621	0.90[AMR][1000 genomes]
rs34669893	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34824628	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35776719	0.93[ASN][1000 genomes]
rs55892665	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56359002	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62165899	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62165905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62165907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6727614	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7569073	1.00[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13429968	VAMP5	cis	lymphoblastoid	seeQTL
rs13429968	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85789400-85803400	Weak transcription	Adipose Nuclei	Adipose
2	chr2:85789400-85803400	Weak transcription	Right Atrium	heart
3	chr2:85789400-85804000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:85791600-85799800	Weak transcription	K562	blood
5	chr2:85797600-85797800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:85797600-85798000	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links