Variant report

Variant	rs2049858
Chromosome Location	chr21:15885274-15885275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:15883124..15887603-chr21:15889415..15891209,4	K562	blood:
2	chr21:15882752..15884455-chr21:15884908..15886969,2	K562	blood:
3	chr21:15878918..15881751-chr21:15882365..15886915,4	K562	blood:
4	chr21:15885068..15887603-chr21:15887779..15891209,3	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1028270	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1028271	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1028273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13046425	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13046549	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13050841	0.88[EUR][1000 genomes]
rs13051840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556278	1.00[ASW][hapmap];0.96[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];1.00[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]
rs1556279	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[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]
rs1556280	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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];0.99[ASN][1000 genomes]
rs2049860	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822706	0.88[CEU][hapmap]
rs2822712	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs2822713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822717	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822718	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822720	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822722	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];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822723	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]
rs2822724	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822725	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822727	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]
rs2822728	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822733	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2822734	0.87[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2822735	0.84[CHB][hapmap]
rs2822740	0.91[GIH][hapmap]
rs2822752	0.85[JPT][hapmap]
rs35382371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35447186	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35778413	0.90[EUR][1000 genomes];0.87[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2049858	SAMSN1	cis	lymphoblastoid	seeQTL
rs2049858	SAMSN1	Cis_1M	lymphoblastoid	RTeQTL
rs2049858	SAMSN1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15853200-15885800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr21:15853400-15905400	Weak transcription	HUVEC	blood vessel
3	chr21:15862600-15889400	Strong transcription	Dnd41	blood
4	chr21:15867000-15890600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr21:15873400-15891000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:15875800-15894000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr21:15877200-15885600	Weak transcription	Gastric	stomach
8	chr21:15878000-15890200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr21:15879200-15892600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr21:15879400-15889400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr21:15879400-15892800	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr21:15879600-15888800	Strong transcription	Primary B cells from cord blood	blood
13	chr21:15879800-15892800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr21:15880800-15892800	Strong transcription	K562	blood
15	chr21:15881600-15891000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr21:15881800-15888800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr21:15881800-15893600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr21:15882000-15888800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr21:15882000-15889000	Strong transcription	Primary hematopoietic stem cells	blood
20	chr21:15882200-15890200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr21:15882800-15887600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr21:15883000-15892800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr21:15883200-15886400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr21:15883200-15892800	Weak transcription	Thymus	Thymus
25	chr21:15883200-15893200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr21:15883200-15898600	Weak transcription	Spleen	Spleen
27	chr21:15883600-15888800	Strong transcription	GM12878-XiMat	blood
28	chr21:15883600-15895200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr21:15883800-15888200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr21:15884000-15888000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr21:15884400-15885600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr21:15884400-15892800	Weak transcription	Fetal Thymus	thymus
33	chr21:15884600-15889200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr21:15885000-15886200	Weak transcription	Primary T cells from cord blood	blood
35	chr21:15885200-15886000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr21:15885200-15886000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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