Variant report

Variant	rs2102423
Chromosome Location	chr1:154916068-154916069
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154915987..154916715-chr1:154971279..154972033,2	K562	blood:
2	chr1:154879702..154880586-chr1:154916023..154916700,2	MCF-7	breast:
3	chr1:154878990..154879698-chr1:154916003..154917099,3	MCF-7	breast:
4	chr1:154915676..154917776-chr1:155030028..155032426,2	MCF-7	breast:
5	chr1:154914807..154916848-chr1:155021073..155023957,2	MCF-7	breast:
6	chr1:154506433..154506946-chr1:154915914..154916857,2	MCF-7	breast:
7	chr1:154908783..154912738-chr1:154912911..154918149,9	K562	blood:
8	chr1:154916052..154916727-chr1:154990126..154990697,2	MCF-7	breast:
9	chr1:154910460..154912318-chr1:154915233..154917355,3	MCF-7	breast:
10	chr1:154641959..154642726-chr1:154915957..154916812,4	MCF-7	breast:
11	chr1:154641835..154642437-chr1:154915935..154916477,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163344	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000270361	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1007170	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10796934	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10796935	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908444	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10908445	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10908446	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10908447	0.91[ASN][1000 genomes]
rs10908448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1109815	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264280	0.81[ASN][1000 genomes]
rs11264281	0.91[ASN][1000 genomes]
rs11264282	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11264283	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11264284	0.93[ASN][1000 genomes]
rs11264286	0.96[YRI][hapmap]
rs11264290	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264291	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12036859	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12069356	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12095061	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130132	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1218582	0.88[YRI][hapmap]
rs12406380	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1580943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1891805	0.96[YRI][hapmap]
rs1976559	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1977879	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061690	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	0.91[ASN][1000 genomes]
rs2174507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2211498	0.92[YRI][hapmap]
rs2335407	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2335408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335409	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240874	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4240875	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4339857	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4578216	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4845398	0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845400	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845677	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs4845678	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4845679	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4845680	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845681	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4845682	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845683	0.93[ASN][1000 genomes]
rs4845685	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845687	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845688	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845689	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845691	0.97[ASN][1000 genomes]
rs4845692	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4845693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845694	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845695	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4845696	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656435	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6656494	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6669791	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6674853	0.97[ASN][1000 genomes]
rs6683557	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6686873	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689022	0.92[YRI][hapmap]
rs6699043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699080	0.85[CEU][hapmap]
rs705094	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72702224	1.00[ASN][1000 genomes]
rs7528532	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7531728	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7539805	0.96[YRI][hapmap]
rs7544528	0.83[ASN][1000 genomes]
rs7553195	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs869506	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs877343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883718	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes]
rs906593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9793588	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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
rs2102423	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154910400-154916600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:154910400-154916600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:154910400-154916800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:154910400-154917000	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:154910400-154920000	Weak transcription	Aorta	Aorta
6	chr1:154910400-154923000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:154910400-154925000	Weak transcription	Psoas Muscle	Psoas
8	chr1:154910600-154916800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:154910600-154927200	Weak transcription	Fetal Kidney	kidney
10	chr1:154910800-154916200	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:154910800-154927200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:154910800-154927200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:154911000-154921400	Weak transcription	NHLF	lung
14	chr1:154911400-154916600	Weak transcription	Fetal Heart	heart
15	chr1:154911400-154917200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:154911800-154927400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:154911800-154927400	Weak transcription	NHEK	skin
18	chr1:154912200-154917600	Enhancers	Adipose Nuclei	Adipose
19	chr1:154912400-154917200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:154912600-154916600	Enhancers	Primary T cells from cord blood	blood
21	chr1:154912600-154916600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:154912600-154916600	Enhancers	Spleen	Spleen
23	chr1:154912600-154917000	Flanking Active TSS	GM12878-XiMat	blood
24	chr1:154912600-154917600	Enhancers	Brain Substantia Nigra	brain
25	chr1:154912600-154917800	Enhancers	Fetal Lung	lung
26	chr1:154912600-154917800	Enhancers	K562	blood
27	chr1:154912600-154919200	Genic enhancers	Fetal Muscle Leg	muscle
28	chr1:154912800-154917800	Enhancers	Stomach Mucosa	stomach
29	chr1:154913000-154916400	Weak transcription	Hela-S3	cervix
30	chr1:154913000-154920000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:154913000-154927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:154913200-154916800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:154913200-154927400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:154913400-154917800	Enhancers	Fetal Intestine Large	intestine
35	chr1:154913400-154923000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:154913400-154925600	Weak transcription	Brain Germinal Matrix	brain
37	chr1:154913400-154927000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:154913600-154916200	Weak transcription	Small Intestine	intestine
39	chr1:154913600-154916800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:154913600-154916800	Enhancers	Brain Hippocampus Middle	brain
41	chr1:154913600-154918000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:154913800-154916800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:154913800-154916800	Genic enhancers	Thymus	Thymus
44	chr1:154913800-154917800	Enhancers	Placenta	Placenta
45	chr1:154913800-154918600	Enhancers	Liver	Liver
46	chr1:154914000-154916200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:154914000-154916400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr1:154914000-154927400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:154914200-154916200	Weak transcription	Fetal Stomach	stomach
50	chr1:154914200-154917000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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