Variant report

Variant	rs6683557
Chromosome Location	chr1:154852307-154852308
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154850719..154853708-chr1:154868283..154870650,2	MCF-7	breast:
2	chr1:154849815..154852371-chr1:154881627..154884570,2	MCF-7	breast:
3	chr1:154843876..154848485-chr1:154848730..154854790,7	K562	blood:
4	chr1:154850056..154852682-chr1:154903933..154905463,2	MCF-7	breast:
5	chr1:154850801..154853684-chr1:154854424..154857585,3	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1007170	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10796934	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796935	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908444	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908445	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908446	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908447	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908448	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1109815	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11264278	0.88[ASN][1000 genomes]
rs11264280	0.84[ASN][1000 genomes]
rs11264281	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264282	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264283	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264284	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264290	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12036859	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12069356	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12095061	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12130132	0.90[ASN][1000 genomes]
rs12406380	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1580943	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1976559	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1977879	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2061690	0.85[ASN][1000 genomes]
rs2102423	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2135219	0.95[ASN][1000 genomes]
rs2174507	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2335407	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2335408	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2335409	0.86[ASN][1000 genomes]
rs3738026	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4240874	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4240875	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4339857	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845398	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845400	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845677	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845678	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845679	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845680	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845681	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845682	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845683	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845685	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845687	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845688	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845689	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845690	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845691	0.90[ASN][1000 genomes]
rs4845692	0.86[AMR][1000 genomes]
rs4845693	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4845694	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4845695	0.85[ASN][1000 genomes]
rs4845696	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6656435	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6656494	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6669791	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6674853	0.90[ASN][1000 genomes]
rs6686873	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6699043	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6699080	0.82[AMR][1000 genomes]
rs705094	0.85[ASN][1000 genomes]
rs72702224	0.86[ASN][1000 genomes]
rs7528532	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7531728	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544528	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7553195	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs869506	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs877343	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs883718	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs906593	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9793588	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv432953	chr1:154820067-154855055	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	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
8	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6683557	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154843200-154854200	Weak transcription	Fetal Kidney	kidney
2	chr1:154843200-154854200	Weak transcription	Right Atrium	heart
3	chr1:154850200-154852800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:154850400-154853800	Weak transcription	K562	blood
5	chr1:154850400-154857800	Weak transcription	Lung	lung
6	chr1:154851000-154857800	Weak transcription	Ovary	ovary
7	chr1:154851200-154853200	Weak transcription	Fetal Stomach	stomach
8	chr1:154851200-154856400	Weak transcription	Pancreas	Pancrea
9	chr1:154851400-154853000	Weak transcription	Brain Germinal Matrix	brain
10	chr1:154851400-154854000	Weak transcription	HMEC	breast
11	chr1:154851600-154853400	Weak transcription	Fetal Brain Male	brain
12	chr1:154851600-154853800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:154851800-154853400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:154851800-154853800	Weak transcription	Fetal Brain Female	brain
15	chr1:154851800-154854600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:154852200-154852400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:154852200-154852800	Active TSS	Spleen	Spleen
18	chr1:154852200-154853200	Weak transcription	Brain Cingulate Gyrus	brain

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