Variant report

Variant	rs2822749
Chromosome Location	chr21:15900198-15900199
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:15898174..15900938-chr21:15917034..15919951,2	K562	blood:

Variant related genes	Relation type
ENSG00000155307	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2064022	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2223091	0.95[JPT][hapmap]
rs2822750	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4817234	0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs4817235	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4817236	0.90[JPT][hapmap]
rs6516877	0.95[JPT][hapmap]
rs7280738	0.95[JPT][hapmap]
rs7281104	0.95[JPT][hapmap]
rs9979080	0.97[ASN][1000 genomes]
rs9982259	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9982591	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv913406	chr21:15875108-15905580	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv1796464	chr21:15884475-15900198	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv1800015	chr21:15884475-15906590	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv913408	chr21:15885274-15905580	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv913409	chr21:15885274-15908642	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv459097	chr21:15886919-15902978	Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv587045	chr21:15886919-15902978	Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv459098	chr21:15886919-15906590	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv587046	chr21:15886919-15906590	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv913410	chr21:15889553-15906590	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	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
17	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
18	nsv587047	chr21:15896422-15906590	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2822749	SAMSN1	cis	lymphoblastoid	seeQTL
rs2822749	SAMSN1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15853400-15905400	Weak transcription	HUVEC	blood vessel
2	chr21:15896200-15904200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr21:15896200-15906200	Weak transcription	Fetal Thymus	thymus
4	chr21:15897400-15901600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr21:15897400-15902200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr21:15898600-15900200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr21:15898600-15901000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr21:15898600-15901000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr21:15898800-15900200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr21:15899400-15900600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr21:15899600-15900600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr21:15899800-15901200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr21:15899800-15901400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr21:15899800-15902000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr21:15899800-15906000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr21:15900000-15900200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr21:15900000-15900600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr21:15900000-15900600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr21:15900000-15900600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr21:15900000-15900600	Active TSS	GM12878-XiMat	blood
21	chr21:15900000-15900800	Enhancers	Dnd41	blood
22	chr21:15900000-15900800	Active TSS	K562	blood
23	chr21:15900000-15901000	Enhancers	Primary T cells from cord blood	blood
24	chr21:15900000-15901200	Enhancers	Primary B cells from peripheral blood	blood
25	chr21:15900000-15901600	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr21:15900000-15901800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr21:15900000-15902200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr21:15900000-15904200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr21:15900000-15905200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr21:15900000-15906000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr21:15900000-15906000	Weak transcription	Duodenum Mucosa	Duodenum

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