Variant report

Variant	rs2054728
Chromosome Location	chr2:55818419-55818420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55818262..55820533-chr2:55847496..55849858,2	MCF-7	breast:
2	chr2:55813293..55814824-chr2:55818333..55821254,2	MCF-7	breast:
3	chr2:55818159..55820480-chr2:55842688..55844777,2	K562	blood:
4	chr2:55805782..55807351-chr2:55817870..55819389,2	K562	blood:
5	chr2:55816894..55821327-chr2:55821705..55825491,6	K562	blood:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10496050	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1058582	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11125581	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs17278044	0.81[AMR][1000 genomes]
rs17369191	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17798852	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1823893	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1975484	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1975487	0.91[AFR][1000 genomes]
rs2586947	0.83[AFR][1000 genomes]
rs2586968	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2586969	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2586970	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627759	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2627780	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627782	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35504023	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3762513	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4290693	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4312532	0.90[AFR][1000 genomes]
rs4672054	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4672055	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4672056	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs55761024	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs58003472	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62165173	0.83[AMR][1000 genomes]
rs62165181	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs62165182	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62165183	0.82[AMR][1000 genomes]
rs62165184	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62165196	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62165197	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62165200	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545506	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6744213	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7582278	0.82[AMR][1000 genomes]
rs7594279	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7598650	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs782586	0.80[AFR][1000 genomes]
rs782595	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs782599	0.83[AFR][1000 genomes]
rs782600	0.83[AFR][1000 genomes]
rs782601	0.83[AFR][1000 genomes]
rs782602	0.83[AFR][1000 genomes]
rs782613	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935177	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][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	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	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
4	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
5	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
6	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
7	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
8	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
rs2054728	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:55788800-55825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:55789800-55822800	Weak transcription	HSMMtube	muscle
6	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
9	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
10	chr2:55790800-55819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:55794400-55825200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:55794400-55829000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:55796800-55823800	Weak transcription	Thymus	Thymus
14	chr2:55796800-55825200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:55796800-55825600	Weak transcription	Pancreas	Pancrea
16	chr2:55796800-55829400	Weak transcription	Esophagus	oesophagus
17	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:55797000-55824200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:55797000-55828000	Weak transcription	Aorta	Aorta
20	chr2:55797000-55829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:55797000-55829600	Weak transcription	Gastric	stomach
22	chr2:55801400-55820000	Weak transcription	Ovary	ovary
23	chr2:55803000-55838800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:55803200-55823800	Weak transcription	Lung	lung
25	chr2:55803400-55821200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:55804000-55824000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:55804200-55820600	Weak transcription	Left Ventricle	heart
28	chr2:55804400-55825200	Weak transcription	K562	blood
29	chr2:55806200-55820600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:55806600-55825600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:55806800-55825200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:55807400-55823000	Weak transcription	Fetal Kidney	kidney
33	chr2:55808200-55824800	Weak transcription	Colonic Mucosa	Colon
34	chr2:55809600-55820600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:55809800-55818800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:55810600-55829600	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:55811000-55818600	Strong transcription	Fetal Intestine Large	intestine
38	chr2:55811400-55829400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:55811600-55825000	Weak transcription	Fetal Brain Female	brain
40	chr2:55812400-55819000	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:55812400-55823400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:55812600-55823000	Weak transcription	Fetal Lung	lung
43	chr2:55813000-55820600	Weak transcription	Brain Angular Gyrus	brain
44	chr2:55813400-55819000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:55814200-55820400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:55814200-55822400	Weak transcription	Primary B cells from cord blood	blood
47	chr2:55814200-55825200	Weak transcription	HUVEC	blood vessel
48	chr2:55814200-55825600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:55814200-55829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:55814200-55829400	Weak transcription	Brain Germinal Matrix	brain

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