Variant report

Variant	rs782622
Chromosome Location	chr2:55905122-55905123
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55900455..55903347-chr2:55904036..55907328,3	K562	blood:
2	chr2:55904255..55906446-chr2:55915981..55918234,2	K562	blood:
3	chr2:55903431..55905646-chr2:55905764..55908923,3	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10460508	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1084525	0.85[AMR][1000 genomes]
rs12617719	0.83[AFR][1000 genomes]
rs2586952	0.80[AMR][1000 genomes]
rs2586954	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2627765	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2627766	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2627767	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2627769	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2627772	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2627773	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627779	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62165255	0.82[AMR][1000 genomes]
rs782566	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs782567	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs782568	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782572	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782573	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782579	0.85[ASN][1000 genomes]
rs782584	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs782585	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs782606	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs782619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782629	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782630	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782632	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs782633	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782634	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs782637	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs782641	0.85[AMR][1000 genomes]
rs782642	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782644	0.80[AMR][1000 genomes]
rs809732	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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	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
2	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
3	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
4	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
5	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
6	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
7	esv2760573	chr2:55903016-55941440	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	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
rs782622	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	chr2:55846800-55919800	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	chr2:55864400-55919600	Weak transcription	NHLF	lung
6	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
11	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
12	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
13	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
14	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
15	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
16	chr2:55879000-55917600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:55879400-55914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:55881200-55913000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:55882200-55909600	Weak transcription	Brain Germinal Matrix	brain
20	chr2:55883000-55906800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:55883000-55919800	Weak transcription	HSMMtube	muscle
22	chr2:55883200-55906600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:55883400-55906800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:55888000-55907200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:55888800-55905200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:55888800-55909600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:55889800-55918400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:55890200-55915600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:55890400-55914200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:55892000-55914000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:55892200-55914000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:55892400-55905800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:55892400-55919800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:55892600-55917000	Strong transcription	Dnd41	blood
35	chr2:55893200-55908800	Strong transcription	Osteobl	bone
36	chr2:55893200-55915800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:55893800-55907000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:55893800-55909800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:55893800-55910200	Weak transcription	Colonic Mucosa	Colon
40	chr2:55894000-55905400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:55894000-55919800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:55894200-55909400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:55894400-55905400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:55894400-55906800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:55894600-55906000	Weak transcription	Psoas Muscle	Psoas
46	chr2:55894600-55908200	Weak transcription	Thymus	Thymus
47	chr2:55895400-55905400	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:55895800-55907000	Weak transcription	Fetal Lung	lung
49	chr2:55895800-55920000	Weak transcription	Right Ventricle	heart
50	chr2:55896000-55908200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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