Variant report

Variant	rs12482954
Chromosome Location	chr21:46502169-46502170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:46499894..46505152-chr21:46506062..46510299,9	MCF-7	breast:
2	chr21:46499575..46502481-chr21:46547014..46549747,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10222166	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs12482868	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12482952	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12483020	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]
rs12483115	0.87[ASN][1000 genomes]
rs12483279	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]
rs12483312	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12483758	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12627065	0.90[JPT][hapmap]
rs12627151	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1556316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1556318	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1556319	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs17004734	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17004739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17004743	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs17004748	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2838774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838776	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838789	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2838792	0.93[JPT][hapmap]
rs2838801	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2838802	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs2838809	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2838810	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs2838811	0.90[JPT][hapmap]
rs2838812	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs2838816	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs3178603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs367228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs372173	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs372549	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs3746976	0.90[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs3788154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3788164	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3788169	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs3788170	0.90[CHB][hapmap]
rs3788171	0.90[CHB][hapmap]
rs3788181	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs386528	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs390504	0.92[JPT][hapmap]
rs391834	0.80[ASN][1000 genomes]
rs406551	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs412626	0.92[JPT][hapmap]
rs412666	0.92[JPT][hapmap]
rs421643	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs423726	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs428870	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs431529	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs431666	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs431775	0.81[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs437286	0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs439884	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs442380	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs447656	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs454052	0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs6518215	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs6518216	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs6518218	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7275205	1.00[ASN][1000 genomes]
rs7275931	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7277143	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7279808	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs7281718	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7283317	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7283619	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs731248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8127577	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8129934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8130862	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs8132454	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8132752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8134889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs870145	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870350	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870351	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[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	nsv834110	chr21:46316183-46505151	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46495800-46502600	Weak transcription	Colonic Mucosa	Colon
2	chr21:46495800-46506000	Weak transcription	Pancreas	Pancrea
3	chr21:46496200-46506600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr21:46496200-46511600	Weak transcription	Fetal Intestine Small	intestine
5	chr21:46496400-46509000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr21:46496400-46509000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr21:46496400-46511400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr21:46496400-46511400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr21:46496400-46513000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr21:46496600-46511600	Weak transcription	Brain Hippocampus Middle	brain
11	chr21:46496600-46512000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr21:46496600-46516200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr21:46497000-46504600	Weak transcription	Fetal Intestine Large	intestine
14	chr21:46497600-46509200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr21:46498000-46509200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr21:46498600-46502800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr21:46498600-46513000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr21:46499000-46506600	Weak transcription	Fetal Brain Male	brain
19	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
20	chr21:46499800-46507000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr21:46499800-46509200	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr21:46499800-46510400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr21:46500000-46506800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr21:46500200-46503000	Enhancers	Rectal Smooth Muscle	rectum
26	chr21:46500400-46503000	Weak transcription	Psoas Muscle	Psoas
27	chr21:46500800-46508800	Weak transcription	Fetal Brain Female	brain
28	chr21:46501000-46502200	Strong transcription	Adipose Nuclei	Adipose
29	chr21:46501000-46502400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr21:46501000-46502800	Strong transcription	Fetal Muscle Leg	muscle
31	chr21:46501000-46503000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr21:46501000-46503000	Genic enhancers	Muscle Satellite Cultured Cells	--
33	chr21:46501000-46503000	Strong transcription	HepG2	liver
34	chr21:46501000-46506800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr21:46501000-46509000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr21:46501200-46503000	Genic enhancers	Dnd41	blood
37	chr21:46501200-46503200	Strong transcription	Primary B cells from cord blood	blood
38	chr21:46501200-46508600	Strong transcription	Hela-S3	cervix
39	chr21:46501400-46502800	Strong transcription	NHEK	skin
40	chr21:46501400-46503200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr21:46501400-46503200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr21:46501400-46503800	Weak transcription	A549	lung
43	chr21:46501400-46506400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr21:46501600-46502200	Genic enhancers	Right Ventricle	heart
45	chr21:46501600-46502400	Weak transcription	HUVEC	blood vessel
46	chr21:46501600-46502600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr21:46501600-46502800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr21:46501600-46502800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr21:46501600-46503000	Strong transcription	Brain Angular Gyrus	brain
50	chr21:46501600-46503200	Genic enhancers	Fetal Muscle Trunk	muscle

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