Variant report

Variant	rs439884
Chromosome Location	chr21:46533940-46533941
allele	C/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	chr21:46527903..46530135-chr21:46532581..46534213,2	MCF-7	breast:
3	chr21:46493305..46495041-chr21:46533530..46536007,3	K562	blood:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction
ENSG00000235374	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10222166	0.85[JPT][hapmap]
rs12482868	0.84[ASN][1000 genomes]
rs12482952	0.80[ASN][1000 genomes]
rs12482954	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs12483020	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs12483115	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12483279	0.88[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs12483312	0.87[ASN][1000 genomes]
rs12483758	0.87[ASN][1000 genomes]
rs12627151	0.85[JPT][hapmap]
rs1556316	0.92[JPT][hapmap]
rs1556318	0.85[JPT][hapmap];0.82[MEX][hapmap]
rs1556319	0.85[JPT][hapmap]
rs17004734	0.83[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs17004739	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs17004743	0.85[JPT][hapmap]
rs17004748	0.85[JPT][hapmap]
rs2838774	0.88[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2838776	0.85[ASN][1000 genomes]
rs2838786	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2838789	0.83[CHB][hapmap];0.92[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];0.82[MEX][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];0.85[ASN][1000 genomes]
rs367228	0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs372173	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs372549	0.85[JPT][hapmap]
rs3746976	0.85[JPT][hapmap]
rs3788154	0.87[ASN][1000 genomes]
rs3788155	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs3788156	0.88[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs3788163	0.92[CHD][hapmap];0.92[JPT][hapmap]
rs3788164	0.92[JPT][hapmap]
rs3788169	0.85[JPT][hapmap]
rs3788181	0.85[JPT][hapmap]
rs386528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390504	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs391834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs406551	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs412626	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs412666	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs421643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs428870	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs431529	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs442380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447656	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454052	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6518215	0.85[JPT][hapmap]
rs6518216	0.85[JPT][hapmap];0.82[MEX][hapmap]
rs6518218	0.85[JPT][hapmap]
rs7275205	0.87[ASN][1000 genomes]
rs7275931	0.82[ASN][1000 genomes]
rs7277143	0.85[JPT][hapmap]
rs7279808	0.82[JPT][hapmap]
rs7281718	0.82[ASN][1000 genomes]
rs7283317	0.85[JPT][hapmap]
rs7283619	0.85[ASN][1000 genomes]
rs731248	0.92[JPT][hapmap]
rs8129934	0.92[JPT][hapmap]
rs8130862	0.83[JPT][hapmap]
rs8132752	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs8134889	0.92[JPT][hapmap]
rs870145	0.88[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs870350	0.85[ASN][1000 genomes]
rs870351	0.92[JPT][hapmap];0.85[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

No data

Chromatin state (count:81 , 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	chr21:46525200-46534000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr21:46525800-46534000	Weak transcription	HMEC	breast
6	chr21:46526400-46534000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr21:46526400-46549400	Weak transcription	Brain Substantia Nigra	brain
8	chr21:46526800-46536400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr21:46528800-46536600	Genic enhancers	HSMM	muscle
10	chr21:46528800-46537200	Enhancers	Left Ventricle	heart
11	chr21:46529200-46536600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:46529200-46537400	Weak transcription	Ovary	ovary
13	chr21:46529200-46538400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr21:46529400-46534600	Weak transcription	Pancreas	Pancrea
15	chr21:46529400-46540400	Weak transcription	Gastric	stomach
16	chr21:46529400-46549400	Weak transcription	Esophagus	oesophagus
17	chr21:46529600-46534000	Weak transcription	Aorta	Aorta
18	chr21:46529600-46537200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr21:46529800-46554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr21:46530200-46534200	Enhancers	Fetal Heart	heart
21	chr21:46530400-46534200	Weak transcription	Fetal Brain Male	brain
22	chr21:46530400-46538600	Weak transcription	Fetal Kidney	kidney
23	chr21:46530400-46548400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr21:46530400-46554600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr21:46530800-46534000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr21:46530800-46535400	Enhancers	Spleen	Spleen
27	chr21:46530800-46535600	Enhancers	Right Ventricle	heart
28	chr21:46530800-46554600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr21:46531000-46537000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr21:46531200-46534000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr21:46531200-46534200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr21:46531200-46535400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr21:46531200-46536400	Enhancers	Primary B cells from cord blood	blood
34	chr21:46531200-46538800	Enhancers	Primary B cells from peripheral blood	blood
35	chr21:46531200-46542400	Weak transcription	Thymus	Thymus
36	chr21:46531400-46549600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr21:46531800-46535200	Enhancers	Colon Smooth Muscle	Colon
38	chr21:46531800-46541800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr21:46531800-46548200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr21:46531800-46548200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr21:46531800-46548600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr21:46532000-46534000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr21:46532000-46534200	Enhancers	GM12878-XiMat	blood
44	chr21:46532000-46535000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr21:46532200-46534000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr21:46532600-46534200	Enhancers	Fetal Muscle Leg	muscle
47	chr21:46532600-46534200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr21:46532600-46537800	Weak transcription	Primary T cells from cord blood	blood
49	chr21:46532600-46542000	Weak transcription	Fetal Thymus	thymus
50	chr21:46532600-46545200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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