Variant report

Variant	rs17004590
Chromosome Location	chr21:45037289-45037290
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	chr21:45029752..45032331-chr21:45036634..45039497,2	MCF-7	breast:
2	chr21:44935247..44938888-chr21:45036868..45039173,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10427514	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs10483077	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10483078	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs11089065	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11089090	0.91[YRI][hapmap]
rs11908893	0.86[AFR][1000 genomes]
rs11908919	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909195	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909530	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909813	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909916	0.83[AMR][1000 genomes]
rs11909999	0.92[AMR][1000 genomes]
rs11910220	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11910351	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11910352	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11911293	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11911483	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11911560	0.83[AFR][1000 genomes]
rs11911735	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11911856	0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12106371	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12106423	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12106466	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs13339951	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004507	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004580	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004581	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004582	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004585	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004586	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004587	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004588	0.86[AFR][1000 genomes]
rs17004589	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004592	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004593	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004594	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004595	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004596	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004600	0.80[YRI][hapmap]
rs17004602	0.80[YRI][hapmap]
rs28431406	0.83[AMR][1000 genomes]
rs28782771	0.83[AMR][1000 genomes]
rs28852206	0.83[AMR][1000 genomes]
rs59298188	0.85[AMR][1000 genomes]
rs9917493	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv1061539	chr21:44915533-45041824	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1067171	chr21:44921187-45039471	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv521700	chr21:44925334-45041790	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	nsv470903	chr21:44925334-45061501	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	nsv459289	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
7	nsv587690	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
8	nsv834106	chr21:44992387-45109489	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv587700	chr21:45007956-45095200	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45030200-45039400	Weak transcription	Right Atrium	heart
2	chr21:45030600-45042000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr21:45031800-45039400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr21:45031800-45039600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr21:45031800-45039800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr21:45032200-45038600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr21:45032200-45039200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:45032200-45039400	Weak transcription	Brain Germinal Matrix	brain
9	chr21:45032200-45040000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr21:45032200-45059200	Weak transcription	Hela-S3	cervix
11	chr21:45033000-45037800	Weak transcription	Fetal Intestine Small	intestine
12	chr21:45033600-45038400	Weak transcription	Duodenum Mucosa	Duodenum

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