Variant report

Variant	rs2822765
Chromosome Location	chr21:15921516-15921517
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	JUND	chr21:15920981-15921808	K562	blood:	n/a	chr21:15921529-15921538
2	JUN	chr21:15921082-15921611	Hela-S3	cervix:	n/a	chr21:15921529-15921538
3	STAT3	chr21:15920590-15922653	MCF10A-Er-Src	breast:	n/a	chr21:15922627-15922639 chr21:15922216-15922236 chr21:15921421-15921432 chr21:15920607-15920616 chr21:15920608-15920617
4	FOS	chr21:15921057-15921787	MCF10A-Er-Src	breast:	n/a	chr21:15921529-15921538
5	STAT3	chr21:15921047-15921859	MCF10A-Er-Src	breast:	n/a	chr21:15921421-15921432
6	STAT3	chr21:15921098-15921676	MCF10A-Er-Src	breast:	n/a	chr21:15921421-15921432
7	FOS	chr21:15920227-15922024	MCF10A-Er-Src	breast:	n/a	chr21:15920606-15920617 chr21:15921529-15921538
8	POLR2A	chr21:15920337-15922766	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr21:15920314-15923142	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr21:15920824-15921585	MCF10A-Er-Src	breast:	n/a	n/a
11	EP300	chr21:15920505-15921612	Hela-S3	cervix:	n/a	chr21:15920883-15920893 chr21:15921356-15921363
12	RAD21	chr21:15921025-15921614	Hela-S3	cervix:	n/a	n/a
13	E2F4	chr21:15921179-15921722	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr21:15920983-15921637	Hela-S3	cervix:	n/a	n/a
15	TBP	chr21:15921091-15921521	Hela-S3	cervix:	n/a	n/a
16	FOS	chr21:15921051-15921624	MCF10A-Er-Src	breast:	n/a	chr21:15921529-15921538
17	FOS	chr21:15920370-15921645	MCF10A-Er-Src	breast:	n/a	chr21:15920606-15920617 chr21:15921529-15921538
18	STAT3	chr21:15920512-15921690	MCF10A-Er-Src	breast:	n/a	chr21:15921421-15921432 chr21:15920607-15920616 chr21:15920608-15920617
19	STAT3	chr21:15921105-15921633	Hela-S3	cervix:	n/a	chr21:15921421-15921432

No.	Distal block	Cell Line	Cell type
1	chr21:15919781..15923280-chr21:15954504..15956620,3	K562	blood:
2	chr21:15919672..15922192-chr21:15926866..15928968,2	K562	blood:
3	chr21:15920124..15923209-chr21:15941679..15944846,3	K562	blood:
4	chr21:15919906..15922793-chr21:15932302..15934213,2	K562	blood:
5	chr21:15920671..15923360-chr21:15929340..15932218,2	K562	blood:
6	chr21:15918667..15923010-chr21:15942455..15946099,5	K562	blood:
7	chr21:15915978..15918625-chr21:15919465..15922478,3	K562	blood:

Variant related genes	Relation type
SAMSN1	TF binding region
ENSG00000155307	Chromatin interaction
ENSG00000223662	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10854319	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11702574	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11909106	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12329657	0.94[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882916	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1882917	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1974155	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs1980955	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1985538	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2064024	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2178933	0.89[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs2178934	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205366	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2223092	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822760	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2822761	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2822762	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822763	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822767	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822776	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2822777	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs3810580	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930263	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs4817247	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4817248	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6516875	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6516876	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275507	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7280293	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7282042	0.87[CHB][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs7510551	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132641	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9980395	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9980490	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9981275	0.91[ASN][1000 genomes]
rs9983245	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059591	chr21:15835325-15969195	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1056423	chr21:15838309-15948474	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv544376	chr21:15855470-15948474	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1065823	chr21:15863224-15948474	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057934	chr21:15863224-15969195	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1058533	chr21:15896056-15948474	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv544377	chr21:15896056-15948474	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active 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	nsv834045	chr21:15900678-16112850	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv834046	chr21:15903792-16077369	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv2763685	chr21:15904945-15933282	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv587048	chr21:15908642-15932610	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv522627	chr21:15908642-15936503	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2822765	SAMSN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15918800-15922400	Enhancers	Primary hematopoietic stem cells	blood
2	chr21:15918800-15922400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr21:15918800-15922400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr21:15918800-15922400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr21:15918800-15923600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr21:15918800-15923600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr21:15918800-15923800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr21:15918800-15927000	Weak transcription	Fetal Thymus	thymus
9	chr21:15919000-15923600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr21:15919000-15923800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr21:15919200-15921600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr21:15919200-15922200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr21:15919400-15921600	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr21:15919400-15922400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr21:15919600-15923600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr21:15920000-15923200	Enhancers	HUVEC	blood vessel
17	chr21:15920200-15921600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr21:15920200-15923000	Enhancers	Hela-S3	cervix
19	chr21:15920400-15921800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr21:15920400-15922200	Enhancers	Primary T cells from cord blood	blood
21	chr21:15920600-15921800	Weak transcription	Dnd41	blood
22	chr21:15920800-15922400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr21:15921000-15921800	Weak transcription	Primary B cells from cord blood	blood
24	chr21:15921000-15922400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr21:15921000-15923200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr21:15921200-15921600	Enhancers	GM12878-XiMat	blood
27	chr21:15921200-15923000	Enhancers	K562	blood
28	chr21:15921400-15921800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr21:15921400-15922200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr21:15921400-15923800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr21:15921400-15924400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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