Variant report

Variant	rs782587
Chromosome Location	chr2:55839990-55839991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10454749	0.81[AMR][1000 genomes]
rs10496050	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1058582	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1084522	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125579	0.80[EUR][1000 genomes]
rs11125581	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17278044	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17369191	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17798852	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1823893	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1975484	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1975487	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2586947	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2586950	0.88[ASN][1000 genomes]
rs2586968	0.81[AMR][1000 genomes]
rs2586969	0.81[AMR][1000 genomes]
rs2586970	0.81[AMR][1000 genomes]
rs2627759	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627775	0.86[ASN][1000 genomes]
rs2627776	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2627777	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2627780	0.81[AMR][1000 genomes]
rs35504023	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3762513	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4290693	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4672052	0.82[EUR][1000 genomes]
rs4672054	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4672055	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4672056	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55761024	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58003472	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62165173	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62165181	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62165182	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62165183	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62165184	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62165196	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165197	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6545506	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6739513	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs706548	0.95[ASN][1000 genomes]
rs7582278	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7594279	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7598650	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs782586	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782588	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782590	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782594	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782595	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782599	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782600	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782601	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782602	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782649	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782650	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782652	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935177	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs782587	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
3	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:55826000-55841600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:55826200-55842600	Weak transcription	Right Ventricle	heart
6	chr2:55826200-55843000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:55828200-55843600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:55829800-55842800	Weak transcription	Colonic Mucosa	Colon
9	chr2:55830400-55841000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:55830400-55842800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:55830400-55843600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:55830400-55843600	Weak transcription	Aorta	Aorta
13	chr2:55832400-55842800	Weak transcription	Lung	lung
14	chr2:55833200-55841000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:55835000-55841000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:55835400-55842800	Weak transcription	Gastric	stomach
17	chr2:55836000-55842600	Weak transcription	Psoas Muscle	Psoas
18	chr2:55836000-55842600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:55836200-55841000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:55836400-55840600	Strong transcription	GM12878-XiMat	blood
21	chr2:55836600-55843600	Weak transcription	Small Intestine	intestine
22	chr2:55836800-55842600	Weak transcription	Right Atrium	heart
23	chr2:55836800-55842800	Weak transcription	Left Ventricle	heart
24	chr2:55836800-55843600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:55837000-55842400	Weak transcription	Fetal Heart	heart
26	chr2:55837400-55841600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:55837400-55842000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:55837400-55842600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr2:55837400-55842600	Strong transcription	Fetal Thymus	thymus
30	chr2:55837600-55840400	Strong transcription	NHEK	skin
31	chr2:55837600-55840800	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:55837600-55842000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:55837600-55842200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:55837600-55842400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:55837600-55842400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr2:55837600-55842400	Strong transcription	HSMM	muscle
37	chr2:55837800-55840200	Strong transcription	Fetal Stomach	stomach
38	chr2:55837800-55840200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:55837800-55840800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr2:55837800-55841400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:55837800-55841600	Weak transcription	Fetal Kidney	kidney
42	chr2:55837800-55842000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:55837800-55842200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:55837800-55842400	Strong transcription	Placenta	Placenta
45	chr2:55837800-55842400	Strong transcription	Osteobl	bone
46	chr2:55837800-55842600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:55837800-55843400	Weak transcription	Stomach Mucosa	stomach
48	chr2:55838000-55840200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:55838000-55840200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:55838000-55840200	Strong transcription	Fetal Muscle Trunk	muscle

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