Variant report

Variant	rs58854038
Chromosome Location	chr3:50584059-50584060
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50542747..50545519-chr3:50583462..50585219,2	MCF-7	breast:
2	chr3:50574960..50577068-chr3:50582421..50584590,2	K562	blood:
3	chr3:50376122..50377896-chr3:50582869..50585002,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1038415	1.00[EUR][1000 genomes]
rs107457	1.00[EUR][1000 genomes]
rs1552255	1.00[EUR][1000 genomes]
rs1552256	1.00[EUR][1000 genomes]
rs17051012	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051016	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051017	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051404	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1843073	1.00[EUR][1000 genomes]
rs2232251	1.00[EUR][1000 genomes]
rs2355337	1.00[EUR][1000 genomes]
rs2459450	1.00[EUR][1000 genomes]
rs2675781	1.00[EUR][1000 genomes]
rs2675785	1.00[EUR][1000 genomes]
rs2675833	1.00[EUR][1000 genomes]
rs407164	1.00[EUR][1000 genomes]
rs421689	1.00[EUR][1000 genomes]
rs4234694	1.00[EUR][1000 genomes]
rs4234695	1.00[EUR][1000 genomes]
rs4267639	1.00[EUR][1000 genomes]
rs4340700	1.00[EUR][1000 genomes]
rs4560294	1.00[AMR][1000 genomes]
rs4688704	1.00[EUR][1000 genomes]
rs55723661	1.00[AMR][1000 genomes]
rs55852678	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56112107	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56198179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56413944	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57077411	1.00[AMR][1000 genomes]
rs57155820	1.00[AMR][1000 genomes]
rs57756789	1.00[EUR][1000 genomes]
rs57867785	1.00[AMR][1000 genomes]
rs57987466	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58231937	1.00[AMR][1000 genomes]
rs58911362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59065723	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59337835	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59340349	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59486246	1.00[AMR][1000 genomes]
rs60132317	1.00[EUR][1000 genomes]
rs60455882	1.00[EUR][1000 genomes]
rs609678	1.00[EUR][1000 genomes]
rs61032466	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61455710	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs621975	1.00[EUR][1000 genomes]
rs628865	1.00[EUR][1000 genomes]
rs650473	1.00[EUR][1000 genomes]
rs665943	1.00[EUR][1000 genomes]
rs6768539	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789552	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833231	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833232	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833239	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833242	1.00[AMR][1000 genomes]
rs73833247	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833248	1.00[AMR][1000 genomes]
rs73833404	1.00[AMR][1000 genomes]
rs73833406	1.00[AMR][1000 genomes]
rs73833886	1.00[AMR][1000 genomes]
rs73833935	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835518	1.00[EUR][1000 genomes]
rs73835533	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835535	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835537	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835538	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936714	1.00[EUR][1000 genomes]
rs9840476	1.00[EUR][1000 genomes]
rs9857033	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
6	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
15	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50577400-50586400	Weak transcription	Brain Anterior Caudate	brain
2	chr3:50578600-50595800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:50579600-50584400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:50583200-50584200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:50583600-50586400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:50583600-50587000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:50583600-50603400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:50583800-50584200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:50583800-50586800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:50583800-50586800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:50583800-50587000	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links