Variant report

Variant	rs2822723
Chromosome Location	chr21:15895685-15895686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:15893314..15896057-chr21:15897268..15899492,2	K562	blood:
2	chr21:15889503..15891554-chr21:15895441..15898226,3	K562	blood:
3	chr21:15888072..15891465-chr21:15894886..15898226,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AF165138.7.1-4	chr21:15895592-15895715	NONHSAT081164

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1028270	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1028271	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1028273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13046425	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13046549	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13050841	0.88[EUR][1000 genomes]
rs13051840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1556278	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1556279	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1556280	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2049858	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2049860	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822706	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs2822712	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822713	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822714	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822717	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822718	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822720	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2822722	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822733	0.82[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2822734	0.91[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2822735	0.84[CHB][hapmap]
rs2822740	0.88[GIH][hapmap]
rs2822752	0.85[JPT][hapmap]
rs35382371	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35447186	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35778413	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv913405	chr21:15875108-15899085	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv913407	chr21:15885274-15899085	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	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
17	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2822723	SAMSN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15853400-15905400	Weak transcription	HUVEC	blood vessel
2	chr21:15883200-15898600	Weak transcription	Spleen	Spleen
3	chr21:15893000-15896200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr21:15893000-15899400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr21:15893200-15898600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr21:15893400-15896000	Enhancers	Primary B cells from cord blood	blood
7	chr21:15893400-15896200	Enhancers	Primary B cells from peripheral blood	blood
8	chr21:15894000-15897800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr21:15894200-15899200	Weak transcription	Thymus	Thymus
10	chr21:15894800-15896200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr21:15895000-15896200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr21:15895000-15896200	Enhancers	Fetal Thymus	thymus
13	chr21:15895200-15895800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr21:15895200-15895800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr21:15895200-15896000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr21:15895200-15896000	Enhancers	Small Intestine	intestine
17	chr21:15895200-15896200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr21:15895200-15896200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr21:15895200-15896200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr21:15895200-15896200	Enhancers	Duodenum Mucosa	Duodenum
21	chr21:15895200-15896200	Flanking Active TSS	Dnd41	blood
22	chr21:15895200-15896600	Flanking Active TSS	GM12878-XiMat	blood
23	chr21:15895200-15897400	Genic enhancers	K562	blood
24	chr21:15895400-15895800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr21:15895400-15895800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr21:15895400-15896000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr21:15895400-15896000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr21:15895400-15896200	Enhancers	Primary T cells from cord blood	blood
29	chr21:15895400-15896200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr21:15895600-15895800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr21:15895600-15895800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr21:15895600-15896000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr21:15895600-15896000	Enhancers	Fetal Kidney	kidney
34	chr21:15895600-15896200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr21:15895600-15896200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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