Variant report

Variant	rs2627778
Chromosome Location	chr2:55866453-55866454
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	chr2:55865013..55867773-chr2:55869528..55871983,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1045910	0.91[CHB][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12474717	0.81[AMR][1000 genomes]
rs12617829	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12619756	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12713301	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12989898	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs13028892	0.83[JPT][hapmap]
rs13427693	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13430657	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1373228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1563201	0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1814457	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1975485	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1975486	0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2168097	0.87[ASN][1000 genomes]
rs2586946	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2586948	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586949	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2586951	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2586953	0.81[ASN][1000 genomes]
rs2586955	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2586958	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2586959	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2586960	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2586961	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2586965	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2627757	0.81[AMR][1000 genomes]
rs2627758	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2627763	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2627768	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2627771	0.85[ASN][1000 genomes]
rs2627774	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2627781	0.87[EUR][1000 genomes]
rs2627783	0.83[ASN][1000 genomes]
rs3748945	0.80[ASN][1000 genomes]
rs58727204	0.81[AMR][1000 genomes]
rs61475257	0.82[ASN][1000 genomes]
rs6545503	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs6545505	0.96[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs6731927	0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs706549	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs706550	0.96[CHB][hapmap];0.96[JPT][hapmap];0.88[ASN][1000 genomes]
rs706551	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72812173	0.81[AMR][1000 genomes]
rs730884	0.83[ASN][1000 genomes]
rs744514	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs7559307	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7571482	0.81[ASN][1000 genomes]
rs7585484	0.95[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7605486	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7605504	0.87[ASN][1000 genomes]
rs782569	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs782570	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782571	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs782574	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782575	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782576	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782577	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782580	1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782582	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782583	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782589	0.91[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782591	0.91[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs782593	0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs782597	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782598	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs782603	0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs782604	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs782612	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782614	0.81[ASN][1000 genomes]
rs782615	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782617	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782618	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782620	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782621	0.91[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782623	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782624	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782625	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782626	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782627	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782628	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs782631	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782635	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782636	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782638	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782643	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782646	0.83[ASN][1000 genomes]
rs782647	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782648	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782651	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9636439	0.83[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2627778	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	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:55847600-55870000	Weak transcription	Colonic Mucosa	Colon
7	chr2:55847600-55870000	Weak transcription	Psoas Muscle	Psoas
8	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
9	chr2:55848000-55872600	Weak transcription	Small Intestine	intestine
10	chr2:55849200-55867400	Weak transcription	Lung	lung
11	chr2:55849200-55868200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:55849200-55868200	Weak transcription	Right Ventricle	heart
13	chr2:55849200-55869400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:55849200-55873200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:55849400-55867400	Weak transcription	Thymus	Thymus
16	chr2:55849800-55869400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:55849800-55882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:55851400-55870000	Weak transcription	Spleen	Spleen
19	chr2:55852000-55872400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:55853600-55882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:55857000-55873800	Strong transcription	Fetal Thymus	thymus
22	chr2:55857600-55869800	Weak transcription	Brain Angular Gyrus	brain
23	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
24	chr2:55858600-55871600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:55858800-55873400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:55858800-55875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:55858800-55877200	Strong transcription	Dnd41	blood
28	chr2:55859000-55876800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:55859000-55877000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:55859000-55877200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:55859200-55874000	Weak transcription	Pancreas	Pancrea
32	chr2:55859400-55875600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:55859400-55877600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:55859800-55871200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:55859800-55871400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:55859800-55873200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:55859800-55873600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
39	chr2:55860600-55869800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:55860800-55871200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:55861800-55868000	Strong transcription	Liver	Liver
42	chr2:55861800-55875000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:55861800-55875800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr2:55862000-55868400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr2:55862000-55873400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:55862000-55874800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr2:55862000-55875000	Strong transcription	Fetal Intestine Large	intestine
48	chr2:55862000-55877200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:55862000-55877800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:55862200-55867400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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