Variant report

Variant	rs11887686
Chromosome Location	chr2:85924131-85924132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNLY-2	chr2:85924111-85924800	NONHSAT072043
2	lnc-GNLY-2	chr2:85924111-85924224	NONHSAT072044

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11885917	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896795	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899443	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17026578	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72926903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73943282	1.00[ASN][1000 genomes]
rs73943284	1.00[ASN][1000 genomes]
rs9309623	0.92[EUR][1000 genomes];1.00[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	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv874465	chr2:85898898-85939207	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv2812	chr2:85899944-85929267	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv874466	chr2:85909026-85939207	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv874467	chr2:85916487-85946708	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11887686	MXRA7	trans	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85920400-85924600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:85920400-85925600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:85921200-85924400	Active TSS	Primary T cells fromperipheralblood	blood
4	chr2:85921800-85926400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:85922000-85931400	Weak transcription	Lung	lung
6	chr2:85922400-85928600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:85922600-85925400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:85922600-85925400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:85922800-85926800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr2:85923000-85927000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr2:85923400-85924400	Weak transcription	Placenta	Placenta
12	chr2:85923600-85924600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:85923600-85925600	Weak transcription	K562	blood
14	chr2:85923800-85924200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr2:85923800-85924600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:85923800-85924800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:85924000-85924200	Weak transcription	Spleen	Spleen
18	chr2:85924000-85924600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:85924000-85924800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:85924000-85925200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:85924000-85925200	Enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links