Variant report

Variant	rs1542506
Chromosome Location	chr9:100160167-100160168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:100139724..100142040-chr9:100160057..100161608,2	MCF-7	breast:
2	chr9:100158859..100160754-chr9:100392262..100394128,2	K562	blood:
3	chr9:100160143..100162987-chr9:100172478..100174284,2	MCF-7	breast:
4	chr9:100158999..100160647-chr9:100162275..100163910,2	MCF-7	breast:
5	chr9:100150282..100151155-chr9:100159898..100160560,2	MCF-7	breast:
6	chr9:100149625..100153516-chr9:100159731..100163036,3	MCF-7	breast:
7	chr9:100150440..100152091-chr9:100159690..100161456,2	MCF-7	breast:
8	chr9:100159957..100161541-chr9:100168022..100169977,2	MCF-7	breast:
9	chr9:100159820..100162414-chr9:100401342..100403835,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196116	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10122063	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10125198	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1020884	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1020885	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1037948	0.89[EUR][1000 genomes]
rs1037950	0.95[EUR][1000 genomes]
rs1037951	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10435868	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10448274	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10759527	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs10759624	0.88[EUR][1000 genomes]
rs10759657	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10817273	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs10817286	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs10817487	0.90[EUR][1000 genomes]
rs10981367	0.80[JPT][hapmap]
rs10981460	0.81[JPT][hapmap]
rs10981890	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs10981919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12377538	0.81[JPT][hapmap]
rs12550923	0.81[JPT][hapmap]
rs12551740	0.81[JPT][hapmap]
rs13287082	0.81[JPT][hapmap]
rs13289134	0.81[JPT][hapmap]
rs1531440	0.81[JPT][hapmap]
rs1947717	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2045729	0.80[JPT][hapmap]
rs2169456	0.96[CEU][hapmap]
rs2242187	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2279114	0.93[EUR][1000 genomes]
rs2290933	0.81[JPT][hapmap]
rs2306094	0.81[JPT][hapmap]
rs2306097	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs3747489	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs3747493	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs3747495	0.80[JPT][hapmap]
rs3747496	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs3747498	0.80[JPT][hapmap]
rs3747499	0.80[JPT][hapmap]
rs3747504	0.80[JPT][hapmap]
rs3747506	0.80[JPT][hapmap]
rs3802471	0.91[EUR][1000 genomes]
rs3994560	0.80[JPT][hapmap]
rs4237189	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4313271	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4366181	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4523385	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4554595	0.89[EUR][1000 genomes]
rs4742685	0.87[EUR][1000 genomes]
rs4742689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4742690	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743070	0.81[JPT][hapmap]
rs4743073	0.81[JPT][hapmap]
rs4743076	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4743077	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4743084	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4743087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4743088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6478095	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs6478131	0.93[EUR][1000 genomes]
rs7869536	0.93[EUR][1000 genomes]
rs9696167	0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036105	chr9:100131266-100171816	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1542506	RP11-520B13.4	cis	Thyroid	GTEx
rs1542506	RP11-498P14.5	cis	lung	GTEx
rs1542506	ANKRD18CP	cis	Thyroid	GTEx
rs1542506	CCDC180	cis	Artery Tibial	GTEx
rs1542506	VN1R51P	cis	Thyroid	GTEx
rs1542506	RP11-23J9.4	cis	Artery Tibial	GTEx
rs1542506	RP11-520B13.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100149600-100161400	Weak transcription	Right Atrium	heart
2	chr9:100157400-100161800	Weak transcription	Thymus	Thymus
3	chr9:100157800-100162000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:100159000-100160400	Weak transcription	HepG2	liver
5	chr9:100159000-100160600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:100159000-100161400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:100159200-100161600	Enhancers	GM12878-XiMat	blood
8	chr9:100159800-100160200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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