Variant report

Variant	rs420499
Chromosome Location	chr21:46551422-46551423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46358799..46362946-chr21:46546409..46551680,5	K562	blood:
2	chr21:46550409..46551930-chr21:46569679..46571872,2	MCF-7	breast:
3	chr21:46386181..46388411-chr21:46549880..46552492,2	MCF-7	breast:
4	chr21:46491911..46497737-chr21:46547142..46552694,13	K562	blood:
5	chr21:46544212..46547881-chr21:46548757..46552730,5	K562	blood:
6	chr21:46492248..46501057-chr21:46545477..46562980,48	K562	blood:
7	chr21:46532796..46535414-chr21:46551102..46553894,2	K562	blood:

Variant related genes	Relation type
ENSG00000235374	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000267857	Chromatin interaction
ENSG00000268856	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs17004494	0.82[EUR][1000 genomes]
rs17004749	0.85[EUR][1000 genomes]
rs17004752	0.85[EUR][1000 genomes]
rs17004754	0.85[EUR][1000 genomes]
rs2032253	1.00[CEU][hapmap]
rs2838772	0.88[EUR][1000 genomes]
rs2838775	1.00[CEU][hapmap]
rs2838779	1.00[CEU][hapmap]
rs2838780	1.00[CEU][hapmap]
rs2838784	1.00[CEU][hapmap]
rs2838785	1.00[CEU][hapmap]
rs373249	0.88[EUR][1000 genomes]
rs375621	0.88[EUR][1000 genomes]
rs377244	0.85[EUR][1000 genomes]
rs387536	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs406923	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs407550	0.85[EUR][1000 genomes]
rs412431	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs414174	0.83[EUR][1000 genomes]
rs422205	0.81[EUR][1000 genomes]
rs423892	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs425176	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs430446	0.85[EUR][1000 genomes]
rs437833	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs444789	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs451550	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs453176	0.85[EUR][1000 genomes]
rs7279483	0.82[EUR][1000 genomes]
rs73232669	0.82[EUR][1000 genomes]
rs73232686	0.85[EUR][1000 genomes]
rs9306119	0.85[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	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv522002	chr21:46542670-46551702	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46529800-46554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr21:46530400-46554600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr21:46530800-46554600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr21:46532600-46552400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr21:46532600-46570600	Weak transcription	Dnd41	blood
6	chr21:46538800-46552200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr21:46541800-46552400	Weak transcription	Fetal Brain Male	brain
8	chr21:46544200-46558200	Weak transcription	HepG2	liver
9	chr21:46544200-46560400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr21:46544400-46552400	Weak transcription	Thymus	Thymus
11	chr21:46545000-46554800	Enhancers	Fetal Muscle Leg	muscle
12	chr21:46545600-46553200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr21:46546600-46554600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr21:46546800-46552800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr21:46546800-46555200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr21:46547200-46552400	Weak transcription	Primary T cells from cord blood	blood
17	chr21:46548200-46553400	Enhancers	Colon Smooth Muscle	Colon
18	chr21:46548200-46553600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr21:46548400-46551800	Enhancers	Rectal Smooth Muscle	rectum
20	chr21:46548600-46551800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr21:46548600-46552200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr21:46548600-46552600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr21:46548600-46554000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr21:46548600-46554400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr21:46548600-46571600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr21:46548800-46554800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr21:46548800-46558400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr21:46549400-46551600	Enhancers	Fetal Stomach	stomach
29	chr21:46549600-46551600	Enhancers	Brain Angular Gyrus	brain
30	chr21:46549800-46551600	Enhancers	Primary hematopoietic stem cells	blood
31	chr21:46549800-46553000	Weak transcription	Esophagus	oesophagus
32	chr21:46549800-46554600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr21:46549800-46554800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr21:46549800-46557200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr21:46549800-46559400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr21:46549800-46567600	Weak transcription	Gastric	stomach
37	chr21:46550000-46552400	Weak transcription	Placenta	Placenta
38	chr21:46550000-46552800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr21:46550000-46552800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr21:46550000-46553400	Weak transcription	Brain Substantia Nigra	brain
41	chr21:46550000-46555800	Weak transcription	Aorta	Aorta
42	chr21:46550000-46567800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr21:46550200-46552600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr21:46550200-46552600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr21:46550200-46552800	Weak transcription	Right Atrium	heart
46	chr21:46550200-46553800	Enhancers	Fetal Muscle Trunk	muscle
47	chr21:46550400-46552400	Weak transcription	Brain Hippocampus Middle	brain
48	chr21:46550400-46571200	Weak transcription	Brain Germinal Matrix	brain
49	chr21:46550600-46552800	Weak transcription	Stomach Mucosa	stomach
50	chr21:46550800-46551600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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