Variant report

Variant	rs62165181
Chromosome Location	chr2:55778350-55778351
allele	C/T
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:
2	chr2:55745086..55746689-chr2:55776287..55778878,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10454749	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10496050	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1058582	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1084522	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11125579	0.87[EUR][1000 genomes]
rs11125581	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17278044	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17369191	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17798852	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1823893	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1975484	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1975487	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2054728	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2586947	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2586968	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2586969	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2586970	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2627759	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2627776	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2627777	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2627780	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2627782	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35504023	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3762513	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4290693	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4672052	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4672054	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4672055	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4672056	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55761024	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58003472	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62165173	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62165182	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62165183	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62165184	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62165196	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62165197	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62165200	0.90[AFR][1000 genomes]
rs6545506	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6739513	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6744213	0.81[AFR][1000 genomes]
rs706548	0.85[ASN][1000 genomes]
rs7582278	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7594279	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7598650	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs782586	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782587	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782588	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782590	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782594	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782595	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs782599	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782600	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782601	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782602	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782613	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs782649	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs782650	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782652	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs935177	0.94[AFR][1000 genomes];0.83[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
rs62165181	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr2:55748200-55778800	Weak transcription	Fetal Heart	heart
6	chr2:55748200-55782400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:55752600-55788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
9	chr2:55753600-55786600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:55754000-55784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:55754400-55783000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:55758200-55781200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:55758200-55783800	Weak transcription	Gastric	stomach
14	chr2:55758200-55784000	Weak transcription	Pancreas	Pancrea
15	chr2:55758600-55784000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:55760800-55788000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:55761000-55788200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:55761400-55781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:55762000-55783800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:55762200-55782600	Weak transcription	NHEK	skin
21	chr2:55762200-55784000	Weak transcription	Right Ventricle	heart
22	chr2:55762800-55781000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr2:55765200-55780200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:55766400-55783000	Weak transcription	Fetal Brain Male	brain
25	chr2:55767000-55784000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:55768800-55778400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr2:55769400-55778400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:55769600-55778800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:55769800-55782600	Strong transcription	Fetal Intestine Large	intestine
31	chr2:55769800-55788200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:55770000-55778600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:55770000-55787000	Strong transcription	Dnd41	blood
34	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
35	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr2:55770800-55778600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:55770800-55815800	Strong transcription	Liver	Liver
38	chr2:55771200-55788000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:55771400-55778400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:55771600-55788000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:55771800-55788200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:55772600-55780800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:55772600-55788000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:55772800-55781400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:55772800-55782600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:55773000-55779800	Weak transcription	HMEC	breast
47	chr2:55773000-55780600	Weak transcription	Fetal Brain Female	brain
48	chr2:55773000-55784000	Weak transcription	Aorta	Aorta
49	chr2:55773200-55780200	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:55773200-55783800	Weak transcription	Rectal Smooth Muscle	rectum

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