Variant report

Variant	rs2822767
Chromosome Location	chr21:15923039-15923040
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	MYC	chr21:15922554-15923076	K562	blood:	n/a	n/a
2	EP300	chr21:15922561-15923113	K562	blood:	n/a	chr21:15922779-15922788
3	RCOR1	chr21:15922597-15923133	K562	blood:	n/a	n/a
4	POLR2A	chr21:15920314-15923142	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:15919781..15923280-chr21:15954504..15956620,3	K562	blood:
2	chr21:15922292..15924126-chr21:15926793..15928319,2	K562	blood:
3	chr21:15920124..15923209-chr21:15941679..15944846,3	K562	blood:
4	chr21:15915915..15920125-chr21:15922754..15925442,5	K562	blood:
5	chr21:15920671..15923360-chr21:15929340..15932218,2	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	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11702574	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11909106	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12329657	0.89[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882916	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1882917	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1974155	0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap]
rs1980955	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1985538	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2064024	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2178933	0.89[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2178934	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205366	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2223092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822760	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2822761	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2822762	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822763	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822765	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];0.89[JPT][hapmap];0.84[TSI][hapmap]
rs2822777	0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap]
rs3810580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930263	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs4817247	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4817248	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6516875	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6516876	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275507	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7280293	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7282042	0.87[CHB][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7510551	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132641	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9980395	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9980490	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9981275	0.91[ASN][1000 genomes]
rs9983245	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];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
rs2822767	SAMSN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15918800-15923600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr21:15918800-15923600	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr21:15918800-15923800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr21:15918800-15927000	Weak transcription	Fetal Thymus	thymus
5	chr21:15919000-15923600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr21:15919000-15923800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr21:15919600-15923600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr21:15920000-15923200	Enhancers	HUVEC	blood vessel
9	chr21:15921000-15923200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr21:15921400-15923800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr21:15921400-15924400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr21:15921800-15923600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr21:15922000-15923600	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr21:15922200-15923400	Enhancers	Primary B cells from cord blood	blood
15	chr21:15922400-15923200	Flanking Active TSS	Dnd41	blood
16	chr21:15922400-15923600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr21:15922400-15923600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr21:15922800-15923400	Enhancers	Primary hematopoietic stem cells	blood
19	chr21:15922800-15923600	Enhancers	Primary T cells from cord blood	blood
20	chr21:15922800-15924000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr21:15923000-15923200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr21:15923000-15923400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr21:15923000-15923600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:15923000-15923800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr21:15923000-15924600	Weak transcription	K562	blood
26	chr21:15923000-15927000	Weak transcription	Primary B cells from peripheral blood	blood

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