Variant report

Variant	rs2627779
Chromosome Location	chr2:55892356-55892357
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	chr2:55891954..55894358-chr2:55898574..55900895,2	K562	blood:
2	chr2:55890547..55892839-chr2:55908611..55911224,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10460508	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1084525	0.82[AFR][1000 genomes]
rs2586950	0.85[AFR][1000 genomes]
rs2586952	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2586954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627759	0.81[EUR][1000 genomes]
rs2627765	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2627766	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2627767	0.85[ASN][1000 genomes]
rs2627769	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2627772	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2627773	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627775	0.81[AFR][1000 genomes]
rs2627776	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2627777	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs782566	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782567	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782568	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782572	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782573	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782579	0.86[ASN][1000 genomes]
rs782584	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs782585	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs782595	0.81[EUR][1000 genomes]
rs782606	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs782619	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782622	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs782629	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782630	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782632	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs782633	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782634	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs782637	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782641	0.83[AFR][1000 genomes]
rs782642	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs782649	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs782650	0.82[EUR][1000 genomes]
rs782652	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs809732	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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	esv2762645	chr2:55892248-55963418	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2627779	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
4	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
5	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:55864400-55919600	Weak transcription	NHLF	lung
7	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:55870600-55892800	Weak transcription	Psoas Muscle	Psoas
10	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:55870800-55893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:55870800-55903600	Weak transcription	Gastric	stomach
13	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
15	chr2:55871000-55893200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:55871000-55893200	Weak transcription	Thymus	Thymus
17	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
18	chr2:55871200-55893400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
20	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
21	chr2:55873200-55893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
23	chr2:55873800-55899400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
25	chr2:55879000-55896200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:55879000-55917600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:55879200-55902800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:55879400-55914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:55881200-55913000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:55881800-55898000	Weak transcription	NHDF-Ad	bronchial
31	chr2:55882000-55893400	Weak transcription	Right Ventricle	heart
32	chr2:55882000-55893400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:55882200-55909600	Weak transcription	Brain Germinal Matrix	brain
34	chr2:55882400-55892600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:55883000-55892400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:55883000-55892600	Weak transcription	Primary B cells from cord blood	blood
37	chr2:55883000-55893400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:55883000-55906800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:55883000-55919800	Weak transcription	HSMMtube	muscle
40	chr2:55883200-55892800	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:55883200-55893200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:55883200-55893400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:55883200-55906600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:55883400-55892600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:55883400-55892800	Weak transcription	Brain Anterior Caudate	brain
46	chr2:55883400-55892800	Weak transcription	NHEK	skin
47	chr2:55883400-55893000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:55883400-55893000	Weak transcription	Placenta	Placenta
49	chr2:55883400-55893000	Weak transcription	NH-A	brain
50	chr2:55883400-55893400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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