Variant report

Variant	rs406923
Chromosome Location	chr21:46538491-46538492
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46531155..46534014-chr21:46536221..46540491,4	K562	blood:
2	chr21:46509836..46512194-chr21:46536516..46538934,2	K562	blood:
3	chr21:46498367..46500555-chr21:46536986..46539536,2	K562	blood:
4	chr21:46537003..46538701-chr21:46539771..46541812,2	K562	blood:
5	chr21:46495410..46497788-chr21:46536429..46538983,2	K562	blood:
6	chr21:46536536..46538761-chr21:46540192..46542423,2	K562	blood:
7	chr21:46497932..46499867-chr21:46537196..46539536,2	K562	blood:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs17004737	1.00[ASN][1000 genomes]
rs17004749	0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs17004752	0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs17004754	0.80[EUR][1000 genomes]
rs2032253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2838772	1.00[CHB][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2838777	1.00[ASN][1000 genomes]
rs2838779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2838780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2838784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2838785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3171490	1.00[ASN][1000 genomes]
rs373249	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377244	0.80[EUR][1000 genomes]
rs387536	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407157	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407550	0.80[EUR][1000 genomes]
rs412431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs413148	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs420499	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs422205	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs423892	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425176	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430446	0.80[EUR][1000 genomes]
rs437833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441788	0.90[LWK][hapmap];1.00[MKK][hapmap]
rs444789	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453176	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs73230662	0.84[ASN][1000 genomes]
rs73230667	1.00[ASN][1000 genomes]
rs73230670	1.00[ASN][1000 genomes]
rs73230679	1.00[ASN][1000 genomes]
rs73230680	1.00[ASN][1000 genomes]
rs73230681	1.00[ASN][1000 genomes]
rs73232640	1.00[ASN][1000 genomes]
rs73232686	0.80[EUR][1000 genomes]
rs8133767	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9306119	0.80[EUR][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:65 , 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	chr21:46523000-46548200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr21:46526400-46549400	Weak transcription	Brain Substantia Nigra	brain
5	chr21:46529400-46540400	Weak transcription	Gastric	stomach
6	chr21:46529400-46549400	Weak transcription	Esophagus	oesophagus
7	chr21:46529800-46554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr21:46530400-46538600	Weak transcription	Fetal Kidney	kidney
9	chr21:46530400-46548400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr21:46530400-46554600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr21:46530800-46554600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr21:46531200-46538800	Enhancers	Primary B cells from peripheral blood	blood
13	chr21:46531200-46542400	Weak transcription	Thymus	Thymus
14	chr21:46531400-46549600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr21:46531800-46541800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr21:46531800-46548200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr21:46531800-46548200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr21:46531800-46548600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr21:46532600-46542000	Weak transcription	Fetal Thymus	thymus
20	chr21:46532600-46545200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr21:46532600-46552400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr21:46532600-46570600	Weak transcription	Dnd41	blood
23	chr21:46532800-46540200	Weak transcription	Adipose Nuclei	Adipose
24	chr21:46532800-46548400	Weak transcription	Osteobl	bone
25	chr21:46533000-46540200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr21:46533800-46542400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr21:46534000-46543000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr21:46534200-46539200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr21:46534600-46540400	Weak transcription	Fetal Brain Male	brain
30	chr21:46534800-46544200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr21:46534800-46545200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr21:46534800-46549600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr21:46535000-46539800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr21:46535000-46544400	Weak transcription	Fetal Stomach	stomach
35	chr21:46535000-46545200	Weak transcription	Psoas Muscle	Psoas
36	chr21:46535200-46539600	Weak transcription	Colon Smooth Muscle	Colon
37	chr21:46535200-46543400	Weak transcription	Fetal Muscle Leg	muscle
38	chr21:46535400-46538600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr21:46535400-46541600	Weak transcription	Fetal Lung	lung
40	chr21:46535400-46542400	Weak transcription	Lung	lung
41	chr21:46535400-46542600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr21:46535400-46544800	Weak transcription	Spleen	Spleen
43	chr21:46535400-46545200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr21:46535600-46538600	Weak transcription	Aorta	Aorta
45	chr21:46536000-46549000	Weak transcription	HMEC	breast
46	chr21:46536200-46546400	Weak transcription	Right Ventricle	heart
47	chr21:46536400-46538800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr21:46536600-46539600	Weak transcription	Hela-S3	cervix
49	chr21:46536600-46540200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr21:46536600-46545200	Strong transcription	HSMM	muscle

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