Variant report

Variant	rs4672054
Chromosome Location	chr2:55773093-55773094
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55771544..55774381-chr2:55776715..55779906,3	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10181648	0.80[EUR][1000 genomes]
rs10454749	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10496050	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1058582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1084522	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11125579	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11125581	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17278044	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17369191	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17798852	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1823893	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1975484	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1975487	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2054728	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2586947	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2586968	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2586969	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2586970	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2627759	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2627776	0.81[EUR][1000 genomes]
rs2627777	0.81[EUR][1000 genomes]
rs2627780	0.82[AMR][1000 genomes]
rs2627782	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35504023	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3762513	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4290693	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4312532	0.87[AFR][1000 genomes]
rs4672052	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4672055	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4672056	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55761024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58003472	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62165173	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62165181	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62165182	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62165183	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62165184	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62165196	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62165197	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6545506	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6739513	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs706548	0.85[ASN][1000 genomes]
rs7582278	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7594279	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7598650	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782586	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782587	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782588	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782590	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782594	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782595	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782599	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782600	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782601	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782602	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782613	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs782649	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782650	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782652	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs935177	0.81[AFR][1000 genomes];0.82[AMR][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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4672054	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
2	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
4	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
5	chr2:55748200-55775800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:55748200-55777400	Weak transcription	NHLF	lung
7	chr2:55748200-55778800	Weak transcription	Fetal Heart	heart
8	chr2:55748200-55782400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:55750000-55775400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:55752600-55788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
12	chr2:55753600-55786600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:55754000-55774600	Weak transcription	Spleen	Spleen
14	chr2:55754000-55784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:55754400-55783000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:55758200-55781200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:55758200-55783800	Weak transcription	Gastric	stomach
18	chr2:55758200-55784000	Weak transcription	Pancreas	Pancrea
19	chr2:55758400-55774000	Weak transcription	Hela-S3	cervix
20	chr2:55758400-55776000	Weak transcription	HUVEC	blood vessel
21	chr2:55758600-55784000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:55759600-55773800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:55760800-55788000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:55761000-55788200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:55761200-55777200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:55761400-55781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:55762000-55783800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:55762200-55782600	Weak transcription	NHEK	skin
29	chr2:55762200-55784000	Weak transcription	Right Ventricle	heart
30	chr2:55762800-55781000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:55763800-55773600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:55765000-55776800	Weak transcription	GM12878-XiMat	blood
33	chr2:55765200-55773200	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:55765200-55780200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:55766400-55783000	Weak transcription	Fetal Brain Male	brain
36	chr2:55766600-55774400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:55767000-55784000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:55768600-55777200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:55768800-55773800	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr2:55768800-55778400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:55769200-55775400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:55769200-55777000	Strong transcription	HSMM	muscle
43	chr2:55769400-55773400	Strong transcription	HSMMtube	muscle
44	chr2:55769400-55773600	Strong transcription	Primary B cells from cord blood	blood
45	chr2:55769400-55774800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr2:55769400-55775000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:55769400-55775400	Strong transcription	Primary hematopoietic stem cells	blood
48	chr2:55769400-55777800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:55769400-55778200	Strong transcription	Adipose Nuclei	Adipose
50	chr2:55769400-55778400	Strong transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links