Variant report

Variant	rs782569
Chromosome Location	chr2:55881816-55881817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1045910	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12617829	0.97[ASN][1000 genomes]
rs12619756	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12713301	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13403782	0.86[ASN][1000 genomes]
rs13427693	0.97[EUR][1000 genomes]
rs13430657	0.97[EUR][1000 genomes]
rs1373228	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1563201	0.81[ASN][1000 genomes]
rs1975485	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1975486	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2168097	0.80[ASN][1000 genomes]
rs2586946	0.86[ASN][1000 genomes]
rs2586948	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2586949	0.81[AMR][1000 genomes]
rs2586951	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586953	0.89[ASN][1000 genomes]
rs2586955	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2586958	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2586959	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2586960	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2586961	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586965	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2627758	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2627763	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2627768	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2627771	0.93[ASN][1000 genomes]
rs2627774	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2627778	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2627781	0.80[EUR][1000 genomes]
rs6545505	0.82[ASN][1000 genomes]
rs6731927	0.81[ASN][1000 genomes]
rs706549	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs706550	0.96[ASN][1000 genomes]
rs706551	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7559307	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571482	0.89[ASN][1000 genomes]
rs7585484	0.80[ASN][1000 genomes]
rs7605486	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7605504	0.80[ASN][1000 genomes]
rs782570	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782571	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782574	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782575	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782576	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs782577	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782580	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782582	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782583	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782589	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs782591	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782593	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782598	0.86[ASN][1000 genomes]
rs782603	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782604	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782605	0.80[EUR][1000 genomes]
rs782612	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782615	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782617	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782618	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782620	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs782621	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs782623	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs782624	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs782625	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782626	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782627	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782628	0.97[ASN][1000 genomes]
rs782631	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782635	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782636	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782638	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782643	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782646	0.90[ASN][1000 genomes]
rs782647	0.93[EUR][1000 genomes]
rs782648	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs782651	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][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	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
4	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
5	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
6	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
7	nsv9791	chr2:55872725-55883751	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs782569	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
4	chr2:55849800-55882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:55853600-55882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
7	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
8	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:55864200-55882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:55864400-55919600	Weak transcription	NHLF	lung
11	chr2:55866200-55882400	Weak transcription	Ovary	ovary
12	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:55870400-55887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:55870400-55887800	Weak transcription	Fetal Brain Female	brain
15	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:55870600-55892800	Weak transcription	Psoas Muscle	Psoas
17	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:55870800-55888000	Weak transcription	Colonic Mucosa	Colon
19	chr2:55870800-55893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:55870800-55903600	Weak transcription	Gastric	stomach
21	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
23	chr2:55871000-55887800	Weak transcription	Esophagus	oesophagus
24	chr2:55871000-55893200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:55871000-55893200	Weak transcription	Thymus	Thymus
26	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
27	chr2:55871200-55893400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
29	chr2:55871400-55882600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
31	chr2:55873000-55888400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:55873200-55893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
34	chr2:55873800-55882600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:55873800-55899400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
37	chr2:55875600-55887200	Weak transcription	K562	blood
38	chr2:55878800-55884400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:55879000-55882000	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:55879000-55882200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:55879000-55882800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:55879000-55883000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr2:55879000-55883000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:55879000-55883200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:55879000-55883200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:55879000-55883400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:55879000-55883400	Strong transcription	Primary T cells from cord blood	blood
48	chr2:55879000-55883400	Strong transcription	A549	lung
49	chr2:55879000-55883600	Strong transcription	Dnd41	blood
50	chr2:55879000-55883800	Strong transcription	Primary T cells fromperipheralblood	blood

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