Variant report

Variant	rs10908447
Chromosome Location	chr1:154869742-154869743
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	chr1:154864032..154866672-chr1:154867262..154870131,3	K562	blood:
2	chr1:154850719..154853708-chr1:154868283..154870650,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1007170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10796934	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10796935	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908444	0.88[ASN][1000 genomes]
rs10908445	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908446	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908448	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1109815	0.91[ASN][1000 genomes]
rs11264276	0.81[AMR][1000 genomes]
rs11264278	0.83[ASN][1000 genomes]
rs11264280	0.89[ASN][1000 genomes]
rs11264281	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264282	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264283	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264284	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264290	0.91[ASN][1000 genomes]
rs12036859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069356	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12095061	0.92[CEU][hapmap];0.91[ASN][1000 genomes]
rs12130132	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12144978	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1580943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976559	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1977879	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2061690	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2102423	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs2135219	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2174507	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2335407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2335408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2335409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3738026	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4240874	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240875	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4339857	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4578216	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4845398	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845399	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845400	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845678	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845680	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845681	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845682	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845683	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845685	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845687	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845688	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845689	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845690	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845691	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845693	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4845694	0.91[ASN][1000 genomes]
rs4845695	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4845696	0.91[ASN][1000 genomes]
rs58629129	0.85[AMR][1000 genomes]
rs6656435	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6656494	0.88[ASN][1000 genomes]
rs6669791	0.91[ASN][1000 genomes]
rs6674853	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6683557	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686873	0.91[ASN][1000 genomes]
rs6699043	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6699080	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs705094	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72702224	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7528532	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544528	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs869506	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877343	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs883718	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs906593	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9793588	0.82[EUR][1000 genomes];0.88[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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv29982	chr1:154818353-154882544	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv464073	chr1:154837796-154904840	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv547960	chr1:154837796-154904840	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10908447	PBXIP1	cis	normal skin	skin_eQTL
rs10908447	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154868200-154869800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:154868400-154869800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr1:154868400-154870000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:154868400-154870000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:154868600-154869800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:154868600-154869800	Enhancers	Brain Germinal Matrix	brain
7	chr1:154868800-154870000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr1:154869400-154869800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:154869400-154869800	Bivalent Enhancer	Fetal Stomach	stomach

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