Variant report

Variant	rs656615
Chromosome Location	chr3:109640548-109640549
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: 63 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1164205	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1164206	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2693621	0.85[ASN][1000 genomes]
rs2693634	0.84[ASN][1000 genomes]
rs2700237	0.84[ASN][1000 genomes]
rs2950151	0.84[ASN][1000 genomes]
rs2950152	0.84[ASN][1000 genomes]
rs581999	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582946	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs586783	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs591010	0.86[ASN][1000 genomes]
rs591350	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs593904	0.84[ASN][1000 genomes]
rs595732	0.84[ASN][1000 genomes]
rs598795	0.84[ASN][1000 genomes]
rs598837	0.84[ASN][1000 genomes]
rs599684	0.84[ASN][1000 genomes]
rs600581	0.84[ASN][1000 genomes]
rs600604	0.84[ASN][1000 genomes]
rs601036	0.84[ASN][1000 genomes]
rs601561	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs604088	0.85[ASN][1000 genomes]
rs605795	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs607043	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs607450	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs610419	0.84[ASN][1000 genomes]
rs614845	0.84[ASN][1000 genomes]
rs617480	0.86[ASN][1000 genomes]
rs619279	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs620727	0.86[ASN][1000 genomes]
rs636972	0.84[ASN][1000 genomes]
rs638718	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs642142	0.84[ASN][1000 genomes]
rs649118	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs652972	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs655376	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs656888	0.88[ASN][1000 genomes]
rs662181	0.84[ASN][1000 genomes]
rs662417	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs666016	0.85[ASN][1000 genomes]
rs667006	0.84[ASN][1000 genomes]
rs671520	0.84[ASN][1000 genomes]
rs686100	0.84[ASN][1000 genomes]
rs686694	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs687239	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs687619	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs687962	0.84[ASN][1000 genomes]
rs688898	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689213	0.84[ASN][1000 genomes]
rs776341	0.82[ASN][1000 genomes]
rs776343	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs776344	0.82[EUR][1000 genomes];0.85[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:11 , 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	chr3:109637800-109640600	Weak transcription	A549	lung
4	chr3:109639800-109641000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:109640000-109640800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:109640400-109640600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:109640400-109640600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:109640400-109640800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:109640400-109640800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:109640400-109640800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:109640400-109640800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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