Variant report

Variant	rs390504
Chromosome Location	chr21:46530945-46530946
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46511460..46514377-chr21:46529611..46531181,2	K562	blood:
2	chr21:46528737..46532394-chr21:46532848..46536874,5	K562	blood:
3	chr21:46515956..46522233-chr21:46528087..46531013,7	K562	blood:
4	chr21:46530815..46533467-chr21:46549475..46551001,2	K562	blood:
5	chr21:46519046..46522635-chr21:46528087..46531462,4	K562	blood:
6	chr21:46527215..46529238-chr21:46529546..46531877,2	MCF-7	breast:
7	chr21:46502343..46504540-chr21:46529179..46531267,2	K562	blood:
8	chr21:46492354..46499042-chr21:46517406..46531809,25	K562	blood:

No data

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

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10222166	0.85[JPT][hapmap]
rs12482954	0.92[JPT][hapmap]
rs12483020	0.92[JPT][hapmap]
rs12483115	0.92[ASN][1000 genomes]
rs12483279	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs12627151	0.85[JPT][hapmap]
rs1556316	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1556318	0.85[JPT][hapmap]
rs1556319	0.85[JPT][hapmap]
rs17004734	0.92[CHD][hapmap];0.92[JPT][hapmap]
rs17004739	0.87[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs17004743	0.85[JPT][hapmap]
rs17004748	0.85[JPT][hapmap]
rs2838774	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs2838786	0.92[JPT][hapmap]
rs2838789	0.81[CEU][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2838792	0.85[JPT][hapmap]
rs2838801	0.84[JPT][hapmap]
rs2838802	0.85[JPT][hapmap]
rs2838809	0.85[JPT][hapmap]
rs2838810	0.85[JPT][hapmap]
rs2838811	0.81[JPT][hapmap]
rs2838812	0.85[JPT][hapmap]
rs2838816	0.85[JPT][hapmap]
rs3178603	0.92[JPT][hapmap]
rs367228	0.85[JPT][hapmap]
rs372173	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs372549	0.85[JPT][hapmap]
rs3746976	0.85[JPT][hapmap]
rs3788155	0.92[JPT][hapmap]
rs3788156	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs3788163	0.92[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs3788164	0.92[JPT][hapmap]
rs3788169	0.85[JPT][hapmap]
rs3788181	0.85[JPT][hapmap]
rs386528	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs391834	0.99[ASN][1000 genomes]
rs406551	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs412626	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412666	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421643	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs423726	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs428870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs431529	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs431666	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs431775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs437286	0.92[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs439884	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs442380	0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs447656	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs454052	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6518215	0.85[JPT][hapmap]
rs6518216	0.85[JPT][hapmap]
rs6518218	0.85[JPT][hapmap]
rs7277143	0.85[JPT][hapmap]
rs7279808	0.82[JPT][hapmap]
rs7283317	0.85[JPT][hapmap]
rs731248	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs8127577	0.84[ASN][1000 genomes]
rs8129934	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs8130862	0.83[JPT][hapmap]
rs8132454	0.84[ASN][1000 genomes]
rs8132752	0.92[JPT][hapmap]
rs8134889	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs870145	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs870351	0.92[JPT][hapmap]

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	nsv3541	chr21:46496415-46536629	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs390504	C21orf33	cis	cerebellum	SCAN
rs390504	HSF2BP	cis	parietal	SCAN
rs390504	MX2	cis	parietal	SCAN
rs390504	SLC19A1	cis	cerebellum	SCAN
rs390504	DNMT3L	cis	parietal	SCAN
rs390504	KRTAP10-7	cis	cerebellum	SCAN

Chromatin state (count:93 , 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	chr21:46522600-46538600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr21:46523000-46532600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr21:46523000-46548200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr21:46525000-46533600	Weak transcription	NHEK	skin
6	chr21:46525200-46534000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr21:46525800-46533600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:46525800-46534000	Weak transcription	HMEC	breast
9	chr21:46526400-46531600	Weak transcription	Hela-S3	cervix
10	chr21:46526400-46533600	Weak transcription	Fetal Stomach	stomach
11	chr21:46526400-46534000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr21:46526400-46549400	Weak transcription	Brain Substantia Nigra	brain
13	chr21:46526800-46531600	Weak transcription	Psoas Muscle	Psoas
14	chr21:46526800-46536400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr21:46527000-46531800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr21:46528600-46531000	Enhancers	HSMMtube	muscle
17	chr21:46528800-46531200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr21:46528800-46531200	Enhancers	Fetal Muscle Trunk	muscle
19	chr21:46528800-46531200	Enhancers	Fetal Muscle Leg	muscle
20	chr21:46528800-46532600	Enhancers	Dnd41	blood
21	chr21:46528800-46536600	Genic enhancers	HSMM	muscle
22	chr21:46528800-46537200	Enhancers	Left Ventricle	heart
23	chr21:46529000-46531000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr21:46529000-46532000	Enhancers	Fetal Lung	lung
25	chr21:46529200-46531000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr21:46529200-46531200	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr21:46529200-46536600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr21:46529200-46537400	Weak transcription	Ovary	ovary
29	chr21:46529200-46538400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr21:46529400-46531400	Bivalent Enhancer	Fetal Thymus	thymus
31	chr21:46529400-46534600	Weak transcription	Pancreas	Pancrea
32	chr21:46529400-46540400	Weak transcription	Gastric	stomach
33	chr21:46529400-46549400	Weak transcription	Esophagus	oesophagus
34	chr21:46529600-46531000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr21:46529600-46531600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr21:46529600-46532200	Enhancers	Rectal Smooth Muscle	rectum
37	chr21:46529600-46534000	Weak transcription	Aorta	Aorta
38	chr21:46529600-46537200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr21:46529800-46531000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr21:46529800-46531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr21:46529800-46531400	Weak transcription	Brain Angular Gyrus	brain
42	chr21:46529800-46531400	Enhancers	Duodenum Mucosa	Duodenum
43	chr21:46529800-46532400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr21:46529800-46554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr21:46530000-46531200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr21:46530000-46531600	Enhancers	Stomach Smooth Muscle	stomach
47	chr21:46530000-46531800	Weak transcription	Colon Smooth Muscle	Colon
48	chr21:46530000-46532600	Enhancers	Primary T cells fromperipheralblood	blood
49	chr21:46530000-46532800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr21:46530000-46532800	Enhancers	Primary T helper cells fromperipheralblood	blood

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