Variant report

Variant	rs12483279
Chromosome Location	chr21:46507697-46507698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46493525..46497229-chr21:46506258..46510035,5	MCF-7	breast:
2	chr21:46499894..46505152-chr21:46506062..46510299,9	MCF-7	breast:
3	chr10:72575676..72576229-chr21:46507484..46507984,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction
ENSG00000166224	Chromatin interaction
ENSG00000235374	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10222166	0.92[JPT][hapmap]
rs12482868	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12482952	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12482954	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12483020	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12483115	0.82[ASN][1000 genomes]
rs12483312	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12483758	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12627065	0.89[JPT][hapmap]
rs12627151	0.87[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs1556316	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1556318	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs1556319	0.92[JPT][hapmap]
rs17004734	0.81[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17004739	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17004743	0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs17004748	0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap]
rs2838774	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838776	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838786	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838789	0.81[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2838792	0.92[JPT][hapmap]
rs2838801	0.92[JPT][hapmap]
rs2838802	0.92[JPT][hapmap]
rs2838809	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs2838810	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs2838811	0.89[JPT][hapmap]
rs2838812	0.92[JPT][hapmap]
rs2838816	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs3178603	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs367228	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs372173	0.92[JPT][hapmap]
rs372549	0.92[JPT][hapmap]
rs3746976	0.92[JPT][hapmap];0.83[EUR][1000 genomes]
rs3788154	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3788155	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788156	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788163	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3788164	1.00[JPT][hapmap]
rs3788169	0.87[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs3788171	0.82[CHD][hapmap];0.90[GIH][hapmap]
rs3788181	0.92[JPT][hapmap]
rs386528	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs390504	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs406551	0.92[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs412626	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs412666	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs421643	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs423726	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs428870	0.88[CHD][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs431529	0.88[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs431666	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs431775	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs437286	0.92[JPT][hapmap]
rs439884	0.88[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs442380	0.92[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs447656	0.88[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs454052	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs6518215	0.92[JPT][hapmap]
rs6518216	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs6518218	0.92[JPT][hapmap]
rs7275205	0.95[ASN][1000 genomes]
rs7275931	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7277143	0.92[JPT][hapmap]
rs7279808	0.90[JPT][hapmap]
rs7281718	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7283317	0.92[JPT][hapmap]
rs7283619	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs731248	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8127577	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8129934	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8130862	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs8132454	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8132752	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8134889	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs870145	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870350	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870351	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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	chr21:46496200-46511600	Weak transcription	Fetal Intestine Small	intestine
2	chr21:46496400-46509000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr21:46496400-46509000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr21:46496400-46511400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr21:46496400-46511400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr21:46496400-46513000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr21:46496600-46511600	Weak transcription	Brain Hippocampus Middle	brain
8	chr21:46496600-46512000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr21:46496600-46516200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr21:46497600-46509200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr21:46498000-46509200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr21:46498600-46513000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
14	chr21:46499800-46509200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr21:46499800-46510400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr21:46500800-46508800	Weak transcription	Fetal Brain Female	brain
18	chr21:46501000-46509000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr21:46501200-46508600	Strong transcription	Hela-S3	cervix
20	chr21:46501600-46508200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr21:46501600-46511200	Weak transcription	Fetal Heart	heart
22	chr21:46501600-46511400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr21:46501600-46513000	Weak transcription	Brain Anterior Caudate	brain
24	chr21:46501800-46509000	Weak transcription	NHLF	lung
25	chr21:46501800-46511400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr21:46502000-46511400	Weak transcription	Gastric	stomach
27	chr21:46502000-46515400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr21:46502000-46516000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr21:46502600-46508800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr21:46502600-46509000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr21:46502600-46511400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr21:46502800-46509400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr21:46503000-46511200	Weak transcription	HSMMtube	muscle
34	chr21:46503000-46511400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr21:46503000-46522200	Weak transcription	Brain Angular Gyrus	brain
36	chr21:46503200-46511400	Weak transcription	Osteobl	bone
37	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr21:46503800-46513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr21:46504200-46508400	Enhancers	Primary B cells from peripheral blood	blood
41	chr21:46504400-46510600	Weak transcription	Fetal Muscle Leg	muscle
42	chr21:46504400-46511200	Weak transcription	HUVEC	blood vessel
43	chr21:46504800-46508200	Enhancers	Right Ventricle	heart
44	chr21:46504800-46508400	Enhancers	Primary B cells from cord blood	blood
45	chr21:46505200-46510600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr21:46506000-46508000	Enhancers	Fetal Thymus	thymus
47	chr21:46506000-46508200	Enhancers	Primary hematopoietic stem cells	blood
48	chr21:46506200-46507800	Enhancers	Spleen	Spleen
49	chr21:46506200-46508000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr21:46506200-46508400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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