Variant report

Variant	rs2823001
Chromosome Location	chr21:16368253-16368254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:16365404..16367302-chr21:16367721..16370714,2	K562	blood:
2	chr21:16361180..16365327-chr21:16366055..16368497,3	K562	blood:
3	chr21:16368212..16371193-chr21:16372878..16374809,2	K562	blood:

Variant related genes	Relation type
ENSG00000180530	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1297215	0.93[EUR][1000 genomes]
rs1810403	0.91[EUR][1000 genomes]
rs2253231	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2253436	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2823000	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517151	0.87[AMR][1000 genomes];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2823001	SAMSN1	cis	cerebellum	SCAN
rs2823001	C21orf81	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16340600-16372800	Weak transcription	GM12878-XiMat	blood
2	chr21:16340600-16374200	Weak transcription	Aorta	Aorta
3	chr21:16340600-16375800	Weak transcription	Right Ventricle	heart
4	chr21:16340800-16368600	Weak transcription	Esophagus	oesophagus
5	chr21:16340800-16373400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr21:16340800-16374400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr21:16340800-16375800	Weak transcription	Gastric	stomach
8	chr21:16340800-16375800	Weak transcription	Lung	lung
9	chr21:16340800-16377600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr21:16341200-16388600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr21:16341600-16377000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr21:16352800-16368600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr21:16354000-16368600	Weak transcription	Spleen	Spleen
14	chr21:16357000-16368600	Weak transcription	Fetal Kidney	kidney
15	chr21:16358800-16377600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr21:16360200-16374200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr21:16360400-16380200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr21:16360400-16402600	Weak transcription	Placenta	Placenta
19	chr21:16360800-16373400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr21:16361600-16369000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr21:16361600-16370800	Weak transcription	Pancreas	Pancrea
22	chr21:16361600-16374600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr21:16361800-16372600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr21:16361800-16374000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr21:16361800-16375800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr21:16362000-16370800	Weak transcription	Colonic Mucosa	Colon
27	chr21:16362200-16373400	Weak transcription	Brain Hippocampus Middle	brain
28	chr21:16362200-16377600	Weak transcription	Fetal Stomach	stomach
29	chr21:16362200-16385800	Weak transcription	K562	blood
30	chr21:16362600-16371600	Weak transcription	Colon Smooth Muscle	Colon
31	chr21:16362600-16374200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr21:16362800-16373400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr21:16363400-16368600	Weak transcription	Ovary	ovary
34	chr21:16363400-16368800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr21:16363400-16383000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr21:16363600-16370400	Weak transcription	Psoas Muscle	Psoas
37	chr21:16363600-16371200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr21:16363600-16373400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr21:16363600-16375800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr21:16363600-16377600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr21:16363600-16377600	Weak transcription	Thymus	Thymus
42	chr21:16363800-16376800	Weak transcription	Dnd41	blood
43	chr21:16364000-16374200	Weak transcription	Primary T cells from cord blood	blood
44	chr21:16364000-16374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr21:16364600-16372400	Weak transcription	Liver	Liver
46	chr21:16364800-16370400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr21:16364800-16370600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr21:16364800-16423000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr21:16365000-16373400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr21:16365200-16368600	Weak transcription	HepG2	liver

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