Variant report

Variant	rs10059953
Chromosome Location	chr5:100128605-100128606
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	chr5:100128599..100130272-chr5:100154288..100156292,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10060686	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10072493	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10072498	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10078934	0.80[CHB][hapmap]
rs11584	0.81[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs11745097	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13358607	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13360613	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs149895	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157042	0.91[ASN][1000 genomes]
rs157043	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157181	0.91[ASN][1000 genomes]
rs17778837	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2544920	0.81[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548256	0.83[EUR][1000 genomes]
rs2548261	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548262	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548264	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548265	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2548274	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548280	0.83[EUR][1000 genomes]
rs2561520	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2725124	0.83[EUR][1000 genomes]
rs276456	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs276457	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs276458	0.91[ASN][1000 genomes]
rs276459	0.91[ASN][1000 genomes]
rs276460	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs276461	0.91[ASN][1000 genomes]
rs276462	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs276465	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs277863	0.86[ASN][1000 genomes]
rs277864	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277865	0.89[ASN][1000 genomes]
rs277866	0.89[ASN][1000 genomes]
rs277867	0.89[ASN][1000 genomes]
rs277868	0.90[ASN][1000 genomes]
rs277869	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277870	0.92[ASN][1000 genomes]
rs277871	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277872	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278493	0.89[ASN][1000 genomes]
rs278494	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278495	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278496	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278497	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278498	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278499	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278500	0.89[ASN][1000 genomes]
rs278501	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278502	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278503	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs278504	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3846626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4702990	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4703115	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4703116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703117	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4703118	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4703119	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55817847	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56165696	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57055845	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6595465	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6864315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6883673	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6886392	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7710701	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7721627	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7736024	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9763775	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	esv2762532	chr5:100041758-100136552	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10059953	SLCO4C1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100114000-100136400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:100126400-100129200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:100126400-100129200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:100127000-100132600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:100128200-100129200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:100128600-100128800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:100128600-100128800	Enhancers	Fetal Lung	lung

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