Variant report

Variant	rs11227689
Chromosome Location	chr11:66874141-66874142
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66873657..66876002-chr11:66881014..66882848,3	MCF-7	breast:
2	chr11:66873988..66875768-chr11:66877376..66880066,2	MCF-7	breast:
3	chr11:66868215..66869893-chr11:66872876..66875422,2	K562	blood:
4	chr11:66873611..66875559-chr11:66884875..66887591,2	K562	blood:
5	chr11:66872090..66874276-chr11:66882740..66884363,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM2A-2	chr11:66873885-66874221	NONHSAT022376

No data

Variant related genes	Relation type
ENSG00000173120	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10791900	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227687	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227695	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227697	0.97[ASN][1000 genomes]
rs11227701	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227703	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227715	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227718	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11227720	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227722	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227732	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11227740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11227745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs11227750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11227751	1.00[AMR][1000 genomes]
rs11227752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs11227755	1.00[JPT][hapmap]
rs11227761	0.87[AMR][1000 genomes]
rs11227765	0.87[AMR][1000 genomes]
rs11227770	0.87[AMR][1000 genomes]
rs12223898	0.87[AMR][1000 genomes]
rs12271777	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12273711	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12274774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12282264	0.83[ASN][1000 genomes]
rs17145414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28604372	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs3892143	0.87[AMR][1000 genomes]
rs55936319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132056	0.87[AMR][1000 genomes]
rs61395951	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61758503	0.87[AMR][1000 genomes]
rs61891311	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61891316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61891317	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61891340	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61891342	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61891343	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61891344	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61891346	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6591234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6591235	0.83[ASN][1000 genomes]
rs7111473	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7127431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs72926981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7927142	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7946985	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7947663	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9630209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv532287	chr11:66784014-67023899	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv365	chr11:66852591-66879246	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv975118	chr11:66862674-66874347	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11227689	RPS6KB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66867800-66880800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:66871600-66884200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:66871800-66875000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:66871800-66875000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr11:66871800-66880400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr11:66872200-66875000	Weak transcription	K562	blood
7	chr11:66873400-66874200	Enhancers	Fetal Thymus	thymus
8	chr11:66873400-66874200	Flanking Active TSS	GM12878-XiMat	blood
9	chr11:66873600-66880400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr11:66873800-66874200	Enhancers	Duodenum Mucosa	Duodenum
11	chr11:66873800-66878400	Weak transcription	Fetal Heart	heart
12	chr11:66873800-66878800	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links