Variant report

Variant	rs2061690
Chromosome Location	chr1:154919080-154919081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154916244..154918003-chr1:154918672..154920315,2	MCF-7	breast:
2	chr1:154912745..154915347-chr1:154916897..154920361,4	MCF-7	breast:
3	chr1:154914226..154915730-chr1:154918870..154920477,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CKS1B-3	chr1:154918040-154919219	NONHSAT006646

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1007170	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs10796934	0.83[ASN][1000 genomes]
rs10796935	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10908445	0.83[ASN][1000 genomes]
rs10908446	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908447	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10908448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1109815	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264281	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11264282	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264283	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264284	0.88[ASN][1000 genomes]
rs11264290	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264291	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12036859	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12069356	0.83[ASN][1000 genomes]
rs12095061	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12130132	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12406380	0.91[EUR][1000 genomes]
rs1580943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1976559	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1977879	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2102423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2135219	0.90[ASN][1000 genomes]
rs2174507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2335407	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2335408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2335409	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3738026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240874	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4240875	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4339857	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4578216	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4845398	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845400	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845677	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845678	0.90[ASN][1000 genomes]
rs4845679	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4845680	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845681	0.85[ASN][1000 genomes]
rs4845682	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845683	0.88[ASN][1000 genomes]
rs4845685	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845687	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845688	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845689	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845691	0.91[ASN][1000 genomes]
rs4845692	0.88[EUR][1000 genomes]
rs4845693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845694	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845695	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4845696	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6656435	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6669791	0.82[ASN][1000 genomes]
rs6674853	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6683557	0.85[ASN][1000 genomes]
rs6686873	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6699043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6699080	0.85[CEU][hapmap];0.84[GIH][hapmap]
rs705094	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72702224	0.95[ASN][1000 genomes]
rs7528532	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7531728	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs7544528	0.82[ASN][1000 genomes]
rs7553195	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs869506	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs877343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs883718	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs906593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9793588	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv872453	chr1:154904840-154995503	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
4	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2061690	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154910400-154920000	Weak transcription	Aorta	Aorta
2	chr1:154910400-154923000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:154910400-154925000	Weak transcription	Psoas Muscle	Psoas
4	chr1:154910600-154927200	Weak transcription	Fetal Kidney	kidney
5	chr1:154910800-154927200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:154910800-154927200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:154911000-154921400	Weak transcription	NHLF	lung
8	chr1:154911800-154927400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:154911800-154927400	Weak transcription	NHEK	skin
10	chr1:154912600-154919200	Genic enhancers	Fetal Muscle Leg	muscle
11	chr1:154913000-154920000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:154913000-154927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:154913200-154927400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:154913400-154923000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:154913400-154925600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:154913400-154927000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:154914000-154927400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:154914200-154927400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:154914400-154920000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:154914400-154923400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:154915000-154920200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:154915000-154920400	Weak transcription	Brain Angular Gyrus	brain
23	chr1:154915200-154927400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:154916000-154920400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:154916200-154920000	Weak transcription	Brain Anterior Caudate	brain
26	chr1:154916400-154919200	Genic enhancers	Fetal Stomach	stomach
27	chr1:154916600-154919400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr1:154916800-154919400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:154916800-154920800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:154916800-154921800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:154916800-154923000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:154916800-154923400	Strong transcription	Primary T cells from cord blood	blood
33	chr1:154916800-154923400	Strong transcription	Thymus	Thymus
34	chr1:154916800-154927200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:154917000-154921200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:154917000-154921400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:154917000-154921800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:154917000-154923000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:154917200-154919400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:154917200-154920800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:154917200-154921000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:154917200-154921000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:154917200-154921200	Strong transcription	HSMMtube	muscle
44	chr1:154917200-154921400	Strong transcription	Lung	lung
45	chr1:154917200-154921600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:154917200-154921600	Strong transcription	Rectal Smooth Muscle	rectum
47	chr1:154917200-154921800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:154917200-154922000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:154917200-154924200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:154917200-154925200	Weak transcription	Small Intestine	intestine

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