Variant report

Variant	rs4845692
Chromosome Location	chr1:154890311-154890312
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10796934	0.86[AMR][1000 genomes]
rs10796935	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10908444	0.81[AMR][1000 genomes]
rs10908445	0.81[AMR][1000 genomes]
rs10908446	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10908448	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1109815	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264282	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11264283	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11264290	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11264291	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12069356	0.81[AMR][1000 genomes]
rs12095061	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12406380	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1580943	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1976559	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1977879	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2061690	0.88[EUR][1000 genomes]
rs2102423	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2174507	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2335408	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3738026	0.86[EUR][1000 genomes]
rs4240874	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4240875	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4339857	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4845398	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845400	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845678	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4845680	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845682	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4845685	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845687	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845688	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4845689	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4845690	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4845693	0.89[EUR][1000 genomes]
rs4845694	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4845696	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6656435	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6683557	0.86[AMR][1000 genomes]
rs6686873	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6699043	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs705094	0.88[EUR][1000 genomes]
rs7528532	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs869506	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs877343	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs883718	0.81[AMR][1000 genomes]
rs906593	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9793588	0.90[AMR][1000 genomes];0.91[EUR][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	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
4	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
5	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
6	nsv2977	chr1:154881053-154907613	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4845692	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154879200-154893200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:154879800-154894800	Weak transcription	Aorta	Aorta
3	chr1:154880400-154894400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:154881400-154894800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:154881600-154895800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:154882200-154891200	Weak transcription	Fetal Stomach	stomach
7	chr1:154882400-154897800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:154882800-154897400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:154883400-154894800	Weak transcription	Primary T cells from cord blood	blood
10	chr1:154883600-154893200	Weak transcription	Liver	Liver
11	chr1:154883600-154895000	Weak transcription	Placenta	Placenta
12	chr1:154883800-154894800	Weak transcription	Brain Germinal Matrix	brain
13	chr1:154884000-154893400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:154884000-154894600	Weak transcription	Gastric	stomach
15	chr1:154884000-154895200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:154884000-154897800	Weak transcription	HMEC	breast
17	chr1:154884600-154894800	Weak transcription	Adipose Nuclei	Adipose
18	chr1:154884800-154894800	Weak transcription	Brain Substantia Nigra	brain
19	chr1:154884800-154894800	Weak transcription	Spleen	Spleen
20	chr1:154884800-154896200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:154884800-154908400	Weak transcription	Psoas Muscle	Psoas
22	chr1:154885000-154892600	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:154885000-154894800	Weak transcription	Esophagus	oesophagus
24	chr1:154885000-154895000	Weak transcription	Brain Anterior Caudate	brain
25	chr1:154885000-154895000	Weak transcription	Ovary	ovary
26	chr1:154885200-154892600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:154885200-154895000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:154885400-154894800	Weak transcription	Lung	lung
29	chr1:154885600-154894200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:154885800-154893400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:154885800-154894200	Weak transcription	Fetal Brain Female	brain
32	chr1:154886000-154897200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:154886600-154894800	Weak transcription	Right Ventricle	heart
34	chr1:154886800-154894800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:154886800-154895400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:154886800-154908200	Weak transcription	Fetal Heart	heart
37	chr1:154887200-154890800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:154887200-154894800	Weak transcription	Left Ventricle	heart
39	chr1:154887400-154891200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:154887600-154891000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:154887600-154891000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:154887600-154892000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr1:154887600-154895200	Weak transcription	NHEK	skin
44	chr1:154888000-154894800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:154888000-154894800	Weak transcription	Thymus	Thymus
46	chr1:154889600-154891200	Weak transcription	Fetal Intestine Small	intestine
47	chr1:154889600-154894800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:154889600-154894800	Weak transcription	GM12878-XiMat	blood
49	chr1:154889600-154895000	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:154889600-154895000	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links