Variant report

Variant	rs73380624
Chromosome Location	chr21:47248323-47248324
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	chr21:47242037..47244390-chr21:47248096..47249777,2	MCF-7	breast:
2	chr21:47246654..47249179-chr21:47249623..47252084,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC19A1-3	chr21:47247875-47251155	ENSG00000205424.1
2	lnc-SLC19A1-3	chr21:47247755-47251155	NONHSAT082996

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11908989	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11909079	1.00[AMR][1000 genomes]
rs11909787	1.00[AMR][1000 genomes]
rs11909949	1.00[AMR][1000 genomes]
rs11910200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11910469	1.00[AMR][1000 genomes]
rs11910564	1.00[AMR][1000 genomes]
rs11910565	1.00[AMR][1000 genomes]
rs11910741	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11910904	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11911016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11911051	1.00[AMR][1000 genomes]
rs11911103	1.00[AMR][1000 genomes]
rs11911110	1.00[AMR][1000 genomes]
rs11911278	1.00[AMR][1000 genomes]
rs11911477	1.00[AMR][1000 genomes]
rs11911528	1.00[AMR][1000 genomes]
rs11911547	1.00[AMR][1000 genomes]
rs11911599	1.00[AMR][1000 genomes]
rs11911859	1.00[AMR][1000 genomes]
rs16978611	1.00[EUR][1000 genomes]
rs28684590	1.00[AMR][1000 genomes]
rs2877093	1.00[EUR][1000 genomes]
rs34087732	1.00[AMR][1000 genomes]
rs56789580	1.00[EUR][1000 genomes]
rs57812778	1.00[AMR][1000 genomes]
rs58160661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58393620	1.00[EUR][1000 genomes]
rs58476668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58587005	1.00[AMR][1000 genomes]
rs58614340	1.00[EUR][1000 genomes]
rs59852288	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60300060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60541263	1.00[EUR][1000 genomes]
rs60918845	1.00[EUR][1000 genomes]
rs61151390	1.00[EUR][1000 genomes]
rs61152109	1.00[AMR][1000 genomes]
rs61265907	1.00[EUR][1000 genomes]
rs61398316	1.00[EUR][1000 genomes]
rs61736689	1.00[AMR][1000 genomes]
rs7275801	1.00[AMR][1000 genomes]
rs7275803	1.00[AMR][1000 genomes]
rs7278814	1.00[AMR][1000 genomes]
rs73376613	1.00[EUR][1000 genomes]
rs73376621	1.00[EUR][1000 genomes]
rs73376631	1.00[EUR][1000 genomes]
rs73376653	1.00[EUR][1000 genomes]
rs73376677	1.00[EUR][1000 genomes]
rs73376685	1.00[EUR][1000 genomes]
rs73376697	1.00[EUR][1000 genomes]
rs73378536	1.00[EUR][1000 genomes]
rs73378554	1.00[EUR][1000 genomes]
rs73378560	1.00[EUR][1000 genomes]
rs73378572	1.00[EUR][1000 genomes]
rs73378580	1.00[EUR][1000 genomes]
rs73378582	1.00[EUR][1000 genomes]
rs73378589	1.00[EUR][1000 genomes]
rs73378591	1.00[EUR][1000 genomes]
rs73378594	1.00[EUR][1000 genomes]
rs73378597	1.00[EUR][1000 genomes]
rs73378599	1.00[EUR][1000 genomes]
rs73380609	1.00[EUR][1000 genomes]
rs73380618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380620	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380625	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380629	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380634	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380636	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380639	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380641	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380652	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380656	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380665	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380668	1.00[EUR][1000 genomes]
rs73380670	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380673	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380675	1.00[EUR][1000 genomes]
rs73380682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73380693	1.00[AMR][1000 genomes]
rs73382504	1.00[EUR][1000 genomes]
rs73382531	1.00[EUR][1000 genomes]
rs73382578	1.00[EUR][1000 genomes]
rs8127953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8128525	1.00[AMR][1000 genomes]
rs8129037	1.00[EUR][1000 genomes]
rs8129516	1.00[AMR][1000 genomes]
rs8133670	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8133782	1.00[EUR][1000 genomes]
rs9984190	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv914078	chr21:47218744-47311686	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
12	esv2756755	chr21:47243032-47319768	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv2758821	chr21:47243032-47319768	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47217800-47260400	Weak transcription	Right Atrium	heart
2	chr21:47240600-47256600	Weak transcription	Dnd41	blood
3	chr21:47241000-47251800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr21:47241000-47255400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr21:47241200-47250200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr21:47241400-47249600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr21:47241600-47257400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr21:47241800-47257600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr21:47244800-47249200	Strong transcription	Thymus	Thymus
10	chr21:47246800-47248400	Enhancers	Primary B cells from peripheral blood	blood
11	chr21:47247000-47248400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr21:47247000-47248400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr21:47247000-47257600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr21:47247200-47248400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr21:47247200-47249400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:47247200-47257000	Weak transcription	Spleen	Spleen
17	chr21:47247600-47248400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr21:47247600-47249200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr21:47248000-47257200	Weak transcription	Primary T cells from cord blood	blood
20	chr21:47248200-47248800	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links