Variant report

Variant	rs2838788
Chromosome Location	chr21:46542374-46542375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46488526..46490205-chr21:46542349..46544446,2	MCF-7	breast:
2	chr21:46493097..46497182-chr21:46538705..46543454,4	MCF-7	breast:
3	chr21:46493588..46497852-chr21:46541349..46545442,5	K562	blood:
4	chr21:46486040..46487619-chr21:46542225..46544248,2	K562	blood:
5	chr21:46541198..46544422-chr21:46544789..46547564,3	K562	blood:
6	chr21:46497598..46499746-chr21:46541735..46543969,2	K562	blood:
7	chr21:46387326..46389294-chr21:46542023..46543987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction
ENSG00000235374	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12152096	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12185823	0.81[JPT][hapmap]
rs13047803	0.81[JPT][hapmap]
rs1556317	0.80[JPT][hapmap]
rs2003273	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2150439	0.81[JPT][hapmap]
rs2838764	0.85[CEU][hapmap];0.89[MEX][hapmap]
rs2838778	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838787	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838797	0.81[JPT][hapmap]
rs2838803	0.81[JPT][hapmap]
rs2838807	0.85[JPT][hapmap]
rs372766	0.81[JPT][hapmap]
rs377524	0.81[JPT][hapmap]
rs381466	0.85[JPT][hapmap]
rs386762	0.81[JPT][hapmap]
rs422720	0.81[JPT][hapmap]
rs434492	0.81[JPT][hapmap]
rs446158	0.81[JPT][hapmap]
rs7281416	0.81[JPT][hapmap]
rs8128889	0.81[JPT][hapmap]
rs8129315	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8130224	0.81[JPT][hapmap]
rs8133307	0.80[JPT][hapmap]
rs8134789	0.81[JPT][hapmap]
rs983749	0.85[JPT][hapmap]
rs9983296	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9984236	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46516400-46549400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr21:46523000-46548200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr21:46526400-46549400	Weak transcription	Brain Substantia Nigra	brain
4	chr21:46529400-46549400	Weak transcription	Esophagus	oesophagus
5	chr21:46529800-46554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr21:46530400-46548400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr21:46530400-46554600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr21:46530800-46554600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr21:46531200-46542400	Weak transcription	Thymus	Thymus
10	chr21:46531400-46549600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr21:46531800-46548200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr21:46531800-46548200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr21:46531800-46548600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr21:46532600-46545200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr21:46532600-46552400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr21:46532600-46570600	Weak transcription	Dnd41	blood
17	chr21:46532800-46548400	Weak transcription	Osteobl	bone
18	chr21:46533800-46542400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr21:46534000-46543000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr21:46534800-46544200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr21:46534800-46545200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr21:46534800-46549600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr21:46535000-46544400	Weak transcription	Fetal Stomach	stomach
24	chr21:46535000-46545200	Weak transcription	Psoas Muscle	Psoas
25	chr21:46535200-46543400	Weak transcription	Fetal Muscle Leg	muscle
26	chr21:46535400-46542400	Weak transcription	Lung	lung
27	chr21:46535400-46542600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr21:46535400-46544800	Weak transcription	Spleen	Spleen
29	chr21:46535400-46545200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr21:46536000-46549000	Weak transcription	HMEC	breast
31	chr21:46536200-46546400	Weak transcription	Right Ventricle	heart
32	chr21:46536600-46545200	Strong transcription	HSMM	muscle
33	chr21:46537200-46545200	Weak transcription	Left Ventricle	heart
34	chr21:46537400-46544600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr21:46537400-46544800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr21:46537400-46548200	Weak transcription	HUVEC	blood vessel
37	chr21:46537400-46548200	Weak transcription	NHEK	skin
38	chr21:46537600-46548200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr21:46538800-46552200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr21:46539000-46546400	Weak transcription	Fetal Intestine Small	intestine
41	chr21:46539200-46542600	Weak transcription	Fetal Heart	heart
42	chr21:46539600-46546800	Enhancers	Colon Smooth Muscle	Colon
43	chr21:46539800-46546400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr21:46540600-46546800	Weak transcription	Aorta	Aorta
45	chr21:46540600-46549400	Weak transcription	Gastric	stomach
46	chr21:46540800-46543400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr21:46540800-46546600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr21:46541000-46542800	Genic enhancers	HSMMtube	muscle
49	chr21:46541200-46542800	Genic enhancers	Muscle Satellite Cultured Cells	--
50	chr21:46541200-46542800	Enhancers	Brain Germinal Matrix	brain

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