Variant report

Variant	rs2822996
Chromosome Location	chr21:16362311-16362312
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	chr21:16361349..16363526-chr21:16365374..16367228,2	MCF-7	breast:
2	chr21:16361180..16365327-chr21:16366055..16368497,3	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12483192	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12627409	0.86[CEU][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap]
rs1474547	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2822989	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2822990	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2822991	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2822992	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822993	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2822997	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2822999	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823004	0.93[CEU][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2823018	0.86[CEU][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap]
rs2823025	0.90[MKK][hapmap]
rs62220715	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62220718	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7282245	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73170294	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73172318	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs909388	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060151	chr21:16295713-16435497	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv544378	chr21:16295713-16435497	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv834048	chr21:16324481-16489570	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2822996	SAMSN1	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16340600-16367400	Weak transcription	NHDF-Ad	bronchial
2	chr21:16340600-16372800	Weak transcription	GM12878-XiMat	blood
3	chr21:16340600-16374200	Weak transcription	Aorta	Aorta
4	chr21:16340600-16375800	Weak transcription	Right Ventricle	heart
5	chr21:16340800-16362600	Weak transcription	Thymus	Thymus
6	chr21:16340800-16362800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr21:16340800-16363000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr21:16340800-16363200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr21:16340800-16363200	Weak transcription	Psoas Muscle	Psoas
10	chr21:16340800-16368000	Weak transcription	HUVEC	blood vessel
11	chr21:16340800-16368200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr21:16340800-16368600	Weak transcription	Esophagus	oesophagus
13	chr21:16340800-16373400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr21:16340800-16374400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr21:16340800-16375800	Weak transcription	Gastric	stomach
16	chr21:16340800-16375800	Weak transcription	Lung	lung
17	chr21:16340800-16377600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr21:16341200-16388600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr21:16341600-16377000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr21:16342000-16362400	Weak transcription	NHLF	lung
21	chr21:16347600-16364600	Weak transcription	Fetal Intestine Small	intestine
22	chr21:16352800-16368600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr21:16354000-16368600	Weak transcription	Spleen	Spleen
24	chr21:16356400-16363400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr21:16356800-16367000	Weak transcription	NH-A	brain
26	chr21:16357000-16368600	Weak transcription	Fetal Kidney	kidney
27	chr21:16358600-16364800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr21:16358800-16377600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr21:16359200-16363400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr21:16359200-16364600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr21:16359200-16364600	Strong transcription	Liver	Liver
32	chr21:16359400-16363200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr21:16359400-16363600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr21:16359400-16364200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr21:16359600-16363800	Strong transcription	Dnd41	blood
36	chr21:16359600-16364200	Strong transcription	NHEK	skin
37	chr21:16359600-16365000	Strong transcription	Fetal Thymus	thymus
38	chr21:16359600-16366400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr21:16359800-16365600	Strong transcription	Primary B cells from cord blood	blood
40	chr21:16359800-16367400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr21:16360200-16362600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr21:16360200-16364400	Weak transcription	Small Intestine	intestine
43	chr21:16360200-16374200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr21:16360400-16362400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr21:16360400-16380200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr21:16360400-16402600	Weak transcription	Placenta	Placenta
47	chr21:16360800-16373400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr21:16361000-16363600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr21:16361000-16363600	Genic enhancers	Fetal Muscle Leg	muscle
50	chr21:16361000-16364800	Genic enhancers	HepG2	liver

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