Variant report

Variant	rs406551
Chromosome Location	chr21:46517063-46517064
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:46516931-46517199	K562	blood:	n/a	n/a
2	POLR2A	chr21:46517051-46517415	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46515771..46517456-chr21:46546796..46548839,2	K562	blood:
2	chr21:46495351..46497648-chr21:46516468..46519256,2	MCF-7	breast:
3	chr21:46513400..46515958-chr21:46516220..46519288,3	MCF-7	breast:
4	chr21:46515041..46517271-chr21:46546796..46549469,2	K562	blood:
5	chr21:46292807..46295598-chr21:46516051..46518200,2	MCF-7	breast:
6	chr21:46515956..46522233-chr21:46528087..46531013,7	K562	blood:
7	chr21:46493165..46495720-chr21:46513762..46518212,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268805	TF binding region
ENSG00000235374	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000268805	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10222166	0.85[JPT][hapmap]
rs12482868	0.83[ASN][1000 genomes]
rs12482954	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs12483020	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs12483115	0.99[ASN][1000 genomes]
rs12483279	0.92[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs12483312	0.86[ASN][1000 genomes]
rs12483758	0.86[ASN][1000 genomes]
rs12627151	0.85[JPT][hapmap]
rs1556316	0.92[JPT][hapmap]
rs1556318	0.85[JPT][hapmap]
rs1556319	0.85[JPT][hapmap]
rs17004734	0.83[CEU][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17004739	0.82[CHD][hapmap];0.92[JPT][hapmap]
rs17004743	0.85[JPT][hapmap]
rs17004748	0.85[JPT][hapmap]
rs2838774	0.92[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838776	0.84[ASN][1000 genomes]
rs2838786	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838789	0.87[CHD][hapmap];0.92[JPT][hapmap]
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];0.84[ASN][1000 genomes]
rs367228	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs372173	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs372549	0.85[JPT][hapmap]
rs3746976	0.85[JPT][hapmap]
rs3788154	0.86[ASN][1000 genomes]
rs3788155	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs3788156	0.92[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs3788163	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs3788164	0.92[JPT][hapmap]
rs3788169	0.85[JPT][hapmap]
rs3788181	0.85[JPT][hapmap]
rs386528	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs390504	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]
rs391834	0.92[ASN][1000 genomes]
rs412626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs412666	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs421643	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs423726	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs428870	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];0.89[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs431529	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs431666	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs431775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs437286	0.92[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs439884	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs442380	0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs447656	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs454052	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6518215	0.85[JPT][hapmap]
rs6518216	0.85[JPT][hapmap]
rs6518218	0.85[JPT][hapmap]
rs7275205	0.86[ASN][1000 genomes]
rs7275931	0.81[ASN][1000 genomes]
rs7277143	0.85[JPT][hapmap]
rs7279808	0.82[JPT][hapmap]
rs7281718	0.81[ASN][1000 genomes]
rs7283317	0.85[JPT][hapmap]
rs7283619	0.84[ASN][1000 genomes]
rs731248	0.92[JPT][hapmap]
rs8129934	0.92[JPT][hapmap]
rs8130862	0.83[JPT][hapmap]
rs8132752	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs8134889	0.92[JPT][hapmap]
rs870145	0.92[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs870350	0.84[ASN][1000 genomes]
rs870351	0.92[JPT][hapmap];0.84[ASN][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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs406551	ADARB1	cis	lymphoblastoid	seeQTL
rs406551	C21orf33	cis	cerebellum	SCAN
rs406551	HSF2BP	cis	parietal	SCAN
rs406551	DNMT3L	cis	parietal	SCAN
rs406551	SLC19A1	cis	cerebellum	SCAN
rs406551	KRTAP10-7	cis	cerebellum	SCAN
rs406551	MX2	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
2	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr21:46503000-46522200	Weak transcription	Brain Angular Gyrus	brain
4	chr21:46506600-46521400	Weak transcription	NHEK	skin
5	chr21:46509400-46524000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr21:46510600-46519200	Enhancers	Primary B cells from peripheral blood	blood
7	chr21:46511800-46520200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr21:46512000-46521600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr21:46512200-46518000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr21:46512200-46521800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr21:46512200-46522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr21:46512200-46525600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr21:46512800-46520400	Enhancers	Fetal Muscle Leg	muscle
14	chr21:46513000-46517600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr21:46513200-46529200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr21:46513400-46518800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr21:46513400-46521600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr21:46513600-46517200	Weak transcription	Fetal Stomach	stomach
19	chr21:46513600-46517600	Enhancers	Adipose Nuclei	Adipose
20	chr21:46513600-46518600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr21:46513600-46519800	Enhancers	Left Ventricle	heart
22	chr21:46513600-46520800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr21:46513600-46522200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr21:46513600-46522400	Weak transcription	Brain Hippocampus Middle	brain
25	chr21:46513600-46522600	Weak transcription	Aorta	Aorta
26	chr21:46513600-46522600	Weak transcription	Brain Anterior Caudate	brain
27	chr21:46513800-46520400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr21:46513800-46522000	Weak transcription	Stomach Mucosa	stomach
29	chr21:46514200-46518800	Enhancers	Spleen	Spleen
30	chr21:46514200-46525000	Enhancers	Right Ventricle	heart
31	chr21:46514400-46518600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr21:46514600-46522600	Weak transcription	Fetal Thymus	thymus
33	chr21:46514800-46517600	Weak transcription	Fetal Brain Male	brain
34	chr21:46514800-46519200	Genic enhancers	HSMM	muscle
35	chr21:46514800-46522200	Weak transcription	Primary T cells from cord blood	blood
36	chr21:46514800-46523800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr21:46515000-46517600	Weak transcription	Colon Smooth Muscle	Colon
38	chr21:46515000-46518400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr21:46515000-46522200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr21:46515200-46518600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr21:46515200-46521800	Weak transcription	Pancreas	Pancrea
42	chr21:46515200-46522000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr21:46515400-46517400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr21:46515400-46522000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr21:46515600-46522400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr21:46516000-46517400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr21:46516000-46517600	Enhancers	Primary B cells from cord blood	blood
48	chr21:46516200-46517800	Weak transcription	Hela-S3	cervix
49	chr21:46516200-46518200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr21:46516200-46518400	Weak transcription	Fetal Brain Female	brain

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