Variant report

Variant	rs2822761
Chromosome Location	chr21:15916134-15916135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:15915978..15918625-chr21:15919465..15922478,3	K562	blood:
2	chr21:15915395..15917614-chr21:16129062..16131798,2	K562	blood:
3	chr21:15914500..15916247-chr21:15937941..15940190,2	K562	blood:
4	chr21:15915303..15917955-chr21:15967480..15970218,2	K562	blood:
5	chr21:15915915..15918568-chr21:15923468..15925442,2	K562	blood:

Variant related genes	Relation type
ENSG00000228600	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10854319	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11702574	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11909106	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12329657	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12483041	1.00[LWK][hapmap]
rs17208186	1.00[LWK][hapmap]
rs1882916	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1882917	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1974155	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap]
rs1980953	0.88[AFR][1000 genomes]
rs1980955	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985538	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064024	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2178933	0.91[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2178934	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2205366	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs2223092	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2822760	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822762	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2822763	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2822765	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]
rs2822767	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]
rs2822776	0.81[CHB][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap]
rs2822777	0.81[CHB][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap]
rs3810580	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3930263	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs4817247	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4817248	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6516875	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6516876	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7275507	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7280293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282042	0.82[CHB][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7510551	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs760348	1.00[LWK][hapmap]
rs8132641	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9980395	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9980490	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9981275	0.88[ASN][1000 genomes]
rs9983245	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.88[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
rs2822761	SAMSN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15913600-15917000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr21:15913600-15917200	Flanking Active TSS	Dnd41	blood
3	chr21:15913600-15919200	Active TSS	K562	blood
4	chr21:15913800-15917000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr21:15913800-15918000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr21:15914000-15918800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr21:15914000-15919000	Active TSS	GM12878-XiMat	blood
8	chr21:15914200-15918800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr21:15914400-15918000	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr21:15914600-15916200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr21:15914600-15916200	Weak transcription	Right Atrium	heart
12	chr21:15914600-15916400	Weak transcription	Brain Anterior Caudate	brain
13	chr21:15914800-15916200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr21:15914800-15916200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr21:15914800-15916400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr21:15914800-15916400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr21:15914800-15917800	Weak transcription	Thymus	Thymus
18	chr21:15914800-15918600	Active TSS	Primary B cells from cord blood	blood
19	chr21:15915200-15916200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr21:15915200-15916400	Weak transcription	Fetal Thymus	thymus
21	chr21:15915400-15916200	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr21:15915400-15916200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr21:15915400-15916400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr21:15915400-15916400	Weak transcription	HUVEC	blood vessel
25	chr21:15915400-15918400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr21:15915600-15916200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr21:15915600-15916200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr21:15915600-15916200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr21:15915600-15918800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr21:15915800-15916200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr21:15915800-15916200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr21:15915800-15916400	Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr21:15916000-15916200	Enhancers	Primary T cells fromperipheralblood	blood
34	chr21:15916000-15916200	Active TSS	Primary hematopoietic stem cells	blood
35	chr21:15916000-15918600	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr21:15916000-15918600	Active TSS	Adipose Nuclei	Adipose

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