Variant report

Variant	rs688878
Chromosome Location	chr11:67339949-67339950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:67339086..67341329-chr11:67409211..67412100,2	K562	blood:
2	chr11:67339423..67341248-chr11:67342794..67345312,3	K562	blood:
3	chr11:67339734..67342343-chr11:67345681..67348171,3	MCF-7	breast:
4	chr11:67339423..67342315-chr11:67342794..67345312,3	K562	blood:
5	chr11:67338809..67340795-chr11:67349639..67351450,2	K562	blood:
6	chr11:67339832..67340773-chr11:67374066..67374800,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000084207	Chromatin interaction
ENSG00000167792	Chromatin interaction
ENSG00000184224	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11227848	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1254125	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871041	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2169650	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2509725	0.94[JPT][hapmap]
rs34743590	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4930204	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930449	0.81[ASN][1000 genomes]
rs584338	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs593055	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs595262	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs598398	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs601531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs604232	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs604908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs615260	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs627449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629952	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs641544	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];1.00[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs643317	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs644670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs649149	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs655848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591246	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591247	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs661624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs667014	0.84[ASN][1000 genomes]
rs669956	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs676653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs689317	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7128347	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7927381	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
4	nsv897807	chr11:67155210-67414492	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
5	nsv897808	chr11:67155210-67419855	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
6	nsv534229	chr11:67164667-67411909	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
7	esv2422195	chr11:67234322-67626901	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
8	nsv1041988	chr11:67319916-67749246	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv897814	chr11:67339949-67460529	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs688878	GSTP1	Cis_1M	lymphoblastoid	RTeQTL
rs688878	GSTP1	cis	lymphoblastoid	seeQTL
rs688878	GSTP1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67336400-67345200	Weak transcription	Gastric	stomach
2	chr11:67338800-67340200	Enhancers	K562	blood
3	chr11:67339600-67340400	Enhancers	A549	lung
4	chr11:67339800-67340000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr11:67339800-67340000	Flanking Active TSS	Hela-S3	cervix
6	chr11:67339800-67340200	Enhancers	Fetal Intestine Small	intestine
7	chr11:67339800-67341000	Enhancers	GM12878-XiMat	blood
8	chr11:67339800-67341400	Enhancers	Fetal Intestine Large	intestine
9	chr11:67339800-67343200	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links