Variant report

Variant	rs17720662
Chromosome Location	chr3:109640616-109640617
allele	A/G
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	PBX3	chr3:109640323-109640868	SK-N-SH	brain:	n/a	n/a
2	REST	chr3:109640257-109640951	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr3:109640496-109640885	H1-neurons	neurons:	n/a	n/a
4	TCF12	chr3:109640340-109640932	SK-N-SH	brain:	n/a	n/a
5	EP300	chr3:109640393-109640719	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr3:109640471-109640769	H1-neurons	neurons:	n/a	n/a
7	PBX3	chr3:109640337-109640877	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000214380	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10934004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11920111	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11921803	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11924231	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11926268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928295	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12631286	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12635802	0.91[ASN][1000 genomes]
rs12639076	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1464371	0.81[ASN][1000 genomes]
rs1526310	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17663892	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17720523	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28540300	0.91[ASN][1000 genomes]
rs34269140	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3844044	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3844045	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3850565	0.91[ASN][1000 genomes]
rs3850566	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3915172	0.91[ASN][1000 genomes]
rs3915173	0.90[ASN][1000 genomes]
rs55701405	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55840771	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55848294	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55968628	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56100358	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56122872	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56175679	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61733710	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66800491	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66894762	0.91[ASN][1000 genomes]
rs67101148	0.91[ASN][1000 genomes]
rs67243448	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67407655	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765010	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6786269	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6786456	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6786633	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791523	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6803300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804264	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68095772	0.90[ASN][1000 genomes]
rs72949915	0.95[ASN][1000 genomes]
rs73217653	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73217667	0.95[ASN][1000 genomes]
rs73217683	0.91[ASN][1000 genomes]
rs7649120	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9842743	0.91[ASN][1000 genomes]
rs9869678	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009075	chr3:109462019-109800029	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv591270	chr3:109462400-109793785	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv877332	chr3:109575764-110186611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1009550	chr3:109577315-109795453	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1839660	chr3:109591203-109678542	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv829666	chr3:109593745-109768652	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2754434	chr3:109604310-109777310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv236806	chr3:109638554-109647641	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3498433	chr3:109640366-109640865	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
10	esv3498434	chr3:109640366-109640865	Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109630000-109642400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:109637400-109645200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:109639800-109641000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:109640000-109640800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:109640400-109640800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:109640400-109640800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:109640400-109640800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:109640400-109640800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:109640600-109641000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:109640600-109641400	Enhancers	Fetal Lung	lung
11	chr3:109640600-109641600	Enhancers	Dnd41	blood
12	chr3:109640600-109641800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:109640600-109644400	Enhancers	A549	lung

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