Variant report

Variant	rs10058388
Chromosome Location	chr5:49956396-49956397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:49949575..49951807-chr5:49954503..49956971,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10035164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10036060	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10039272	0.95[ASN][1000 genomes]
rs10044566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10051561	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10053011	1.00[CHB][hapmap]
rs10054381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10056836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10059085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10060850	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10065432	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10072398	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10075034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10085036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10755235	1.00[CHB][hapmap]
rs10940472	0.84[ASN][1000 genomes]
rs10940497	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11750241	0.84[ASN][1000 genomes]
rs11750771	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12188262	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12188654	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12654776	0.81[ASN][1000 genomes]
rs13153982	0.84[ASN][1000 genomes]
rs13173734	0.84[ASN][1000 genomes]
rs13361410	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13436520	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs154137	1.00[CHB][hapmap]
rs154138	1.00[CHB][hapmap]
rs16884018	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs169497	0.85[CHB][hapmap]
rs182230	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1839128	1.00[CHB][hapmap]
rs2354525	0.91[ASN][1000 genomes]
rs2548581	0.85[CHB][hapmap]
rs2548582	1.00[JPT][hapmap]
rs2548583	1.00[JPT][hapmap]
rs256340	1.00[CHB][hapmap]
rs256341	1.00[CHB][hapmap]
rs2594706	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs26062	1.00[CHB][hapmap]
rs26065	1.00[CHB][hapmap]
rs26069	1.00[CHB][hapmap]
rs26071	1.00[CHB][hapmap]
rs27389	1.00[CHB][hapmap]
rs27466	0.82[CHB][hapmap]
rs27467	1.00[CHB][hapmap]
rs27468	1.00[CHB][hapmap]
rs27469	1.00[CHB][hapmap]
rs27627	1.00[CHB][hapmap]
rs282550	1.00[CHB][hapmap]
rs282553	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs282557	0.84[ASN][1000 genomes]
rs282561	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs28495689	0.82[ASN][1000 genomes]
rs28505342	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28711235	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs32376	1.00[CHB][hapmap]
rs32404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs32425	1.00[CHB][hapmap]
rs3763367	0.88[ASN][1000 genomes]
rs39613	1.00[CHB][hapmap]
rs42284	1.00[CHB][hapmap]
rs4865628	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs57079776	0.88[ASN][1000 genomes]
rs62366937	0.84[ASN][1000 genomes]
rs6872496	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6890519	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6890869	1.00[CHB][hapmap]
rs73097023	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73101028	0.84[ASN][1000 genomes]
rs73101075	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49949800-49961600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:49950000-49959400	Weak transcription	Primary T cells from cord blood	blood
3	chr5:49950200-49959200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:49953000-49959400	Weak transcription	Stomach Mucosa	stomach
5	chr5:49953000-49961800	Weak transcription	Esophagus	oesophagus
6	chr5:49954200-49958800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr5:49954400-49959200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:49954400-49961000	Weak transcription	Primary B cells from cord blood	blood
9	chr5:49954800-49958800	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links