Variant report

Variant	rs3788164
Chromosome Location	chr21:46556216-46556217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46492190..46501097-chr21:46553481..46562048,38	K562	blood:
2	chr21:46552512..46554278-chr21:46555488..46557400,3	MCF-7	breast:
3	chr21:46376597..46379233-chr21:46555743..46557641,2	K562	blood:
4	chr21:46554334..46556297-chr21:46558986..46561697,3	K562	blood:
5	chr21:46372382..46374637-chr21:46555803..46558629,2	K562	blood:
6	chr21:46546584..46551511-chr21:46553581..46558677,4	K562	blood:
7	chr21:46367892..46370514-chr21:46556035..46557918,2	K562	blood:
8	chr21:46492248..46501057-chr21:46545477..46562980,48	K562	blood:
9	chr21:46548264..46550888-chr21:46555243..46558018,2	MCF-7	breast:
10	chr21:46345835..46349084-chr21:46555674..46558816,3	MCF-7	breast:
11	chr21:46555863..46558704-chr21:46711445..46713394,2	MCF-7	breast:
12	chr21:46554988..46557128-chr21:46559277..46561746,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235374	Chromatin interaction
ENSG00000223768	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000160256	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10222166	0.92[JPT][hapmap]
rs12482868	0.91[AFR][1000 genomes]
rs12482954	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12483020	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12483279	1.00[JPT][hapmap]
rs12627065	0.89[JPT][hapmap]
rs12627151	0.92[JPT][hapmap]
rs1556316	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1556318	0.92[JPT][hapmap]
rs1556319	0.92[JPT][hapmap]
rs17004734	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs17004739	0.82[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17004743	0.92[JPT][hapmap]
rs17004748	0.92[JPT][hapmap]
rs2838774	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap]
rs2838776	0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2838786	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2838789	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2838792	0.92[JPT][hapmap]
rs2838801	0.92[JPT][hapmap]
rs2838802	0.92[JPT][hapmap]
rs2838809	0.92[JPT][hapmap]
rs2838810	0.92[JPT][hapmap]
rs2838811	0.89[JPT][hapmap]
rs2838812	0.92[JPT][hapmap]
rs2838816	0.92[JPT][hapmap]
rs3178603	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs367228	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs372173	0.92[JPT][hapmap]
rs372549	0.92[JPT][hapmap]
rs3746976	0.92[JPT][hapmap]
rs3788155	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs3788156	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3788163	0.82[ASW][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs3788169	0.92[JPT][hapmap]
rs3788181	0.92[JPT][hapmap]
rs386528	0.92[JPT][hapmap]
rs390504	0.92[JPT][hapmap]
rs406551	0.92[JPT][hapmap]
rs412626	0.92[JPT][hapmap]
rs412666	0.92[JPT][hapmap]
rs421643	0.92[JPT][hapmap]
rs423726	0.92[JPT][hapmap]
rs428870	0.92[JPT][hapmap]
rs431529	0.92[JPT][hapmap]
rs431666	0.92[JPT][hapmap]
rs431775	0.92[JPT][hapmap]
rs437286	0.92[JPT][hapmap]
rs439884	0.92[JPT][hapmap]
rs442380	0.92[JPT][hapmap]
rs447656	0.92[JPT][hapmap]
rs454052	0.92[JPT][hapmap]
rs6518215	0.92[JPT][hapmap]
rs6518216	0.92[JPT][hapmap]
rs6518218	0.92[JPT][hapmap]
rs7277143	0.92[JPT][hapmap]
rs7279808	0.90[JPT][hapmap]
rs7281718	0.91[AFR][1000 genomes]
rs7283317	0.92[JPT][hapmap]
rs731248	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs8127577	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs8129934	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs8130862	0.91[JPT][hapmap]
rs8132454	0.91[AFR][1000 genomes]
rs8132752	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs8134889	0.82[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs870145	0.82[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs870350	0.91[AFR][1000 genomes]
rs870351	0.82[CHB][hapmap];1.00[JPT][hapmap]

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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46532600-46570600	Weak transcription	Dnd41	blood
2	chr21:46544200-46558200	Weak transcription	HepG2	liver
3	chr21:46544200-46560400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr21:46548600-46571600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr21:46548800-46558400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr21:46549800-46557200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr21:46549800-46559400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr21:46549800-46567600	Weak transcription	Gastric	stomach
9	chr21:46550000-46567800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr21:46550400-46571200	Weak transcription	Brain Germinal Matrix	brain
11	chr21:46550800-46563600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr21:46551000-46556400	Weak transcription	K562	blood
13	chr21:46551000-46562400	Weak transcription	HMEC	breast
14	chr21:46551200-46557000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr21:46551200-46557000	Strong transcription	Hela-S3	cervix
16	chr21:46551200-46557400	Weak transcription	Fetal Intestine Large	intestine
17	chr21:46551400-46567400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr21:46551600-46557200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr21:46551600-46557400	Weak transcription	Colonic Mucosa	Colon
20	chr21:46551600-46562400	Weak transcription	Brain Angular Gyrus	brain
21	chr21:46551600-46562600	Genic enhancers	HSMM	muscle
22	chr21:46551800-46556800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr21:46551800-46565400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr21:46553400-46556400	Weak transcription	NHLF	lung
25	chr21:46553400-46557200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr21:46553400-46558600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr21:46553400-46561600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr21:46553400-46568600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr21:46553400-46570600	Weak transcription	Esophagus	oesophagus
30	chr21:46553400-46574600	Weak transcription	Fetal Heart	heart
31	chr21:46553600-46556800	Weak transcription	HUVEC	blood vessel
32	chr21:46553600-46557200	Weak transcription	Brain Anterior Caudate	brain
33	chr21:46553600-46558800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr21:46553600-46562600	Weak transcription	Placenta	Placenta
35	chr21:46553600-46563000	Weak transcription	Lung	lung
36	chr21:46553800-46561800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr21:46554200-46557000	Enhancers	Psoas Muscle	Psoas
38	chr21:46554200-46557400	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr21:46554400-46557600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr21:46554600-46556400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr21:46554600-46556400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr21:46554600-46556600	Strong transcription	Spleen	Spleen
43	chr21:46554600-46556800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr21:46554600-46557800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr21:46554800-46556400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr21:46554800-46556600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr21:46554800-46556800	Genic enhancers	Fetal Muscle Leg	muscle
48	chr21:46554800-46558600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr21:46554800-46559200	Strong transcription	Primary B cells from cord blood	blood
50	chr21:46554800-46564600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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