Variant report

Variant	rs12481740
Chromosome Location	chr21:40211903-40211904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40207571..40212513-chr21:40281866..40285274,6	MCF-7	breast:
2	chr21:40203275..40206794-chr21:40210041..40212530,5	MCF-7	breast:
3	chr21:40191810..40193575-chr21:40211576..40213668,2	K562	blood:
4	chr21:40175934..40178688-chr21:40209789..40212200,2	MCF-7	breast:
5	chr21:40205616..40208986-chr21:40210258..40212560,3	MCF-7	breast:
6	chr21:40206775..40209110-chr21:40210646..40213517,2	K562	blood:
7	chr21:40210912..40213065-chr21:40219265..40221347,3	K562	blood:
8	chr21:40209144..40212226-chr21:40213678..40216387,3	K562	blood:
9	chr21:40190407..40192977-chr21:40211375..40214122,2	MCF-7	breast:
10	chr21:40209482..40212563-chr21:40213470..40216289,3	MCF-7	breast:
11	chr21:40211369..40213824-chr21:40223080..40225148,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1000844	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1009121	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1051420	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1051475	0.88[ASN][1000 genomes]
rs1051476	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs11088450	0.88[ASN][1000 genomes]
rs11088451	0.88[ASN][1000 genomes]
rs11088452	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11088453	0.90[ASN][1000 genomes]
rs11088454	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1123350	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11254	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs11701191	0.88[ASN][1000 genomes]
rs11701500	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11702403	0.89[ASN][1000 genomes]
rs12482470	0.88[ASN][1000 genomes]
rs12483746	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12627283	0.88[ASN][1000 genomes]
rs13046853	0.88[ASN][1000 genomes]
rs13047133	0.88[ASN][1000 genomes]
rs13047537	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13047745	0.88[ASN][1000 genomes]
rs13048035	0.86[ASN][1000 genomes]
rs13050340	0.90[ASN][1000 genomes]
rs1571707	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2070531	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs2142035	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836683	0.88[ASN][1000 genomes]
rs2836684	0.88[ASN][1000 genomes]
rs2836685	0.88[ASN][1000 genomes]
rs2836686	0.88[ASN][1000 genomes]
rs2836687	0.88[ASN][1000 genomes]
rs2836688	0.88[ASN][1000 genomes]
rs2836689	0.88[ASN][1000 genomes]
rs2836690	0.88[ASN][1000 genomes]
rs2836691	0.88[ASN][1000 genomes]
rs2836692	0.88[ASN][1000 genomes]
rs2836693	0.88[ASN][1000 genomes]
rs2836694	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2836710	0.96[CEU][hapmap];0.93[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836711	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7282444	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7282723	0.88[ASN][1000 genomes]
rs762386	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs762387	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9941892	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs998855	0.90[ASN][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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40195000-40212600	Weak transcription	Right Atrium	heart
2	chr21:40195200-40213800	Weak transcription	Fetal Kidney	kidney
3	chr21:40196400-40229000	Weak transcription	Right Ventricle	heart
4	chr21:40203800-40225200	Weak transcription	Psoas Muscle	Psoas
5	chr21:40209800-40212200	Enhancers	HepG2	liver
6	chr21:40209800-40212200	Enhancers	HUVEC	blood vessel
7	chr21:40210000-40212200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr21:40210000-40212400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr21:40210000-40212800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr21:40210000-40214000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr21:40210000-40214000	Enhancers	NHEK	skin
12	chr21:40210000-40214200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr21:40210000-40214200	Enhancers	HMEC	breast
14	chr21:40210200-40212200	Enhancers	Fetal Muscle Trunk	muscle
15	chr21:40210200-40212400	Enhancers	NHLF	lung
16	chr21:40210200-40212800	Enhancers	NHDF-Ad	bronchial
17	chr21:40210200-40213800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr21:40210400-40212400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr21:40210400-40212400	Enhancers	HSMM	muscle
20	chr21:40210400-40212600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr21:40210400-40212800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr21:40210600-40212000	Enhancers	Fetal Stomach	stomach
23	chr21:40210600-40212200	Enhancers	HSMMtube	muscle
24	chr21:40210800-40212000	Enhancers	Small Intestine	intestine
25	chr21:40210800-40212400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr21:40211000-40212200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr21:40211000-40212200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr21:40211000-40212200	Enhancers	Fetal Muscle Leg	muscle
29	chr21:40211000-40212200	Flanking Active TSS	Osteobl	bone
30	chr21:40211200-40212000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr21:40211200-40212200	Enhancers	K562	blood
32	chr21:40211800-40212000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr21:40211800-40212000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr21:40211800-40212000	Flanking Active TSS	A549	lung
35	chr21:40211800-40212200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr21:40211800-40212200	Enhancers	Placenta	Placenta
37	chr21:40211800-40212200	Flanking Active TSS	Hela-S3	cervix
38	chr21:40211800-40212200	Flanking Active TSS	NH-A	brain
39	chr21:40211800-40212400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr21:40211800-40213200	Enhancers	Esophagus	oesophagus

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