Variant report

Variant	rs2627780
Chromosome Location	chr2:55827548-55827549
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55827514..55830372-chr2:55836467..55838668,2	MCF-7	breast:
2	chr2:55824426..55829337-chr2:55843280..55847413,6	MCF-7	breast:
3	chr2:55825377..55827590-chr2:55842845..55845281,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10496050	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1058582	0.82[AMR][1000 genomes]
rs1084522	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11125581	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17278044	0.85[AFR][1000 genomes]
rs17798852	0.81[AMR][1000 genomes]
rs1823893	0.82[AMR][1000 genomes]
rs1975484	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2054728	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2586947	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2586950	0.80[AFR][1000 genomes]
rs2586968	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586969	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586970	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627759	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2627776	0.82[AFR][1000 genomes]
rs2627777	0.82[AFR][1000 genomes]
rs2627782	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35504023	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3762513	0.81[AMR][1000 genomes]
rs4290693	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4672054	0.82[AMR][1000 genomes]
rs4672055	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4672056	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs55761024	0.82[AMR][1000 genomes]
rs58003472	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62165173	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62165181	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62165184	0.82[AMR][1000 genomes]
rs62165196	0.81[AMR][1000 genomes]
rs62165197	0.80[AFR][1000 genomes]
rs62165200	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545506	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6739513	0.84[AFR][1000 genomes]
rs6744213	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7582278	0.85[AFR][1000 genomes]
rs7594279	0.83[AMR][1000 genomes]
rs782586	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs782587	0.81[AMR][1000 genomes]
rs782588	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs782590	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs782594	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs782595	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs782599	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs782600	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs782601	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs782602	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs782613	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782649	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs782650	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs782652	0.83[AFR][1000 genomes]
rs935177	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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
rs2627780	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	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
6	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
7	chr2:55794400-55829000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:55796800-55829400	Weak transcription	Esophagus	oesophagus
9	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:55797000-55828000	Weak transcription	Aorta	Aorta
11	chr2:55797000-55829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:55797000-55829600	Weak transcription	Gastric	stomach
13	chr2:55803000-55838800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:55810600-55829600	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:55811400-55829400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:55814200-55829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:55814200-55829400	Weak transcription	Brain Germinal Matrix	brain
18	chr2:55818600-55834400	Weak transcription	Small Intestine	intestine
19	chr2:55818600-55835200	Weak transcription	Psoas Muscle	Psoas
20	chr2:55820200-55831400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:55820400-55830400	Strong transcription	Fetal Intestine Large	intestine
22	chr2:55820600-55830600	Strong transcription	Dnd41	blood
23	chr2:55820600-55832000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:55821400-55831200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:55822000-55827800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr2:55822000-55831200	Strong transcription	Fetal Thymus	thymus
27	chr2:55822200-55829400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr2:55822200-55830600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:55822600-55832400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr2:55822800-55827800	Strong transcription	Liver	Liver
31	chr2:55822800-55830400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:55822800-55830400	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:55822800-55830400	Strong transcription	HepG2	liver
34	chr2:55822800-55830800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:55823000-55829600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:55823000-55830400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:55823000-55830600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:55823000-55830600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr2:55823200-55828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:55823400-55829800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:55823600-55830400	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:55823800-55828800	Weak transcription	HSMM	muscle
43	chr2:55823800-55829400	Weak transcription	Spleen	Spleen
44	chr2:55823800-55830400	Strong transcription	Fetal Intestine Small	intestine
45	chr2:55824400-55837400	Weak transcription	Fetal Kidney	kidney
46	chr2:55825200-55830600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:55825400-55828000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:55825400-55828800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:55825400-55830400	Strong transcription	Fetal Lung	lung
50	chr2:55825600-55829400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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