Variant report

Variant	rs10803946
Chromosome Location	chr2:153033517-153033518
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr2:153031990-153033598	GM12878	blood:	n/a	chr2:153031991-153032004

No.	Distal block	Cell Line	Cell type
1	chr2:153023910..153026125-chr2:153032784..153034657,2	K562	blood:
2	chr2:152684763..152686807-chr2:153031833..153033553,2	MCF-7	breast:
3	chr2:153030659..153033731-chr2:153574261..153576507,5	MCF-7	breast:
4	chr2:153030783..153033861-chr2:153572629..153575835,5	MCF-7	breast:
5	chr2:153031056..153034207-chr2:153571978..153575897,4	K562	blood:
6	chr2:152954463..152956019-chr2:153031201..153033706,2	MCF-7	breast:

Variant related genes	Relation type
STAM2	TF binding region
ENSG00000196504	Chromatin interaction
ENSG00000225214	Chromatin interaction
ENSG00000182389	Chromatin interaction
ENSG00000162980	Chromatin interaction
ENSG00000177917	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10184862	0.87[GIH][hapmap];0.86[MEX][hapmap]
rs10497095	0.94[CEU][hapmap];0.87[YRI][hapmap]
rs10497097	0.84[CEU][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10930939	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs10930959	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs10930967	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11679305	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11694120	0.86[AMR][1000 genomes]
rs11884659	0.85[AMR][1000 genomes]
rs11893841	0.95[CEU][hapmap];0.90[TSI][hapmap]
rs12328733	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12476550	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12612557	0.84[CEU][hapmap];0.90[TSI][hapmap]
rs12613984	0.94[CEU][hapmap]
rs12617696	0.81[MEX][hapmap]
rs12621378	0.81[CEU][hapmap];0.94[TSI][hapmap]
rs12623355	0.94[CEU][hapmap]
rs12693270	0.80[AMR][1000 genomes]
rs12693271	0.80[AMR][1000 genomes]
rs12693293	0.88[EUR][1000 genomes]
rs13003423	0.94[CEU][hapmap]
rs13397314	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2002247	0.86[AMR][1000 genomes]
rs2002558	0.86[CHB][hapmap]
rs28394649	1.00[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs28396364	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28785043	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34233450	0.86[AMR][1000 genomes]
rs34657619	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3768648	0.89[CEU][hapmap];0.93[TSI][hapmap]
rs3768649	0.95[CEU][hapmap];0.87[TSI][hapmap]
rs3768651	0.95[CEU][hapmap];0.94[TSI][hapmap]
rs3887026	0.86[CHB][hapmap]
rs4311022	0.86[CHB][hapmap]
rs4368329	0.95[CEU][hapmap];0.81[LWK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes]
rs4473376	0.94[CEU][hapmap]
rs4522558	0.89[EUR][1000 genomes]
rs4611639	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs4664084	0.95[CEU][hapmap];0.81[LWK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes]
rs4664085	0.95[CEU][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4664089	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4664100	0.86[CHB][hapmap]
rs4664535	0.95[CEU][hapmap]
rs5008216	0.86[CHB][hapmap]
rs62176479	0.80[AMR][1000 genomes]
rs6650779	1.00[CEU][hapmap]
rs6720552	0.84[CEU][hapmap]
rs6722740	0.86[CHB][hapmap]
rs6740224	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs7583872	0.86[CHB][hapmap]
rs7589218	1.00[CHB][hapmap]
rs8179814	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9917198	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv459740	chr2:152986041-153045036	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv583316	chr2:152986041-153045036	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10803946	STAM2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153031000-153033600	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr2:153033200-153033600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:153033200-153033600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr2:153033200-153033600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:153033200-153037200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:153033400-153033600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:153033400-153033600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr2:153033400-153033600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr2:153033400-153033600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:153033400-153033600	Enhancers	Liver	Liver
11	chr2:153033400-153033600	Enhancers	A549	lung
12	chr2:153033400-153033600	Flanking Active TSS	HepG2	liver
13	chr2:153033400-153033800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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