Variant report

Variant	rs782589
Chromosome Location	chr2:55842021-55842022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55841593-55846281	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55645913..55647717-chr2:55840630..55843041,2	K562	blood:
2	chr2:55841795..55844862-chr2:55919047..55922552,3	K562	blood:
3	chr2:55276798..55279791-chr2:55841794..55843892,2	K562	blood:

Variant related genes	Relation type
ENSG00000272606	TF binding region
ENSG00000115355	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000138035	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1037508	0.81[ASN][1000 genomes]
rs10427222	0.81[JPT][hapmap]
rs1045910	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12463766	0.81[ASN][1000 genomes]
rs12617829	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12619756	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713301	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12989898	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs13016772	0.83[ASN][1000 genomes]
rs13028892	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs13427693	0.95[EUR][1000 genomes]
rs13430657	0.95[EUR][1000 genomes]
rs1373228	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1563201	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs17792467	1.00[YRI][hapmap]
rs1814457	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1975485	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1975486	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2168097	0.91[ASN][1000 genomes]
rs2586946	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586948	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2586949	0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2586951	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2586955	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2586958	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2586959	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2586960	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2586961	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2586965	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2627758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2627763	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2627768	0.80[AMR][1000 genomes]
rs2627774	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2627778	0.91[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2627781	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2627783	0.86[ASN][1000 genomes]
rs3748945	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3816489	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4233962	0.81[ASN][1000 genomes]
rs4671248	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs61475257	0.86[ASN][1000 genomes]
rs62165178	0.82[ASN][1000 genomes]
rs6545503	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6545505	0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6716100	0.83[JPT][hapmap]
rs6731927	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs706549	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs706550	0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs706551	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs730884	0.88[ASN][1000 genomes]
rs744514	0.84[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7559307	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7585484	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7605486	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7605504	0.91[ASN][1000 genomes]
rs782569	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs782570	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782571	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782574	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782575	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782576	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782577	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782580	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782582	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782583	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782597	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs782598	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782603	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782604	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782612	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782614	0.85[ASN][1000 genomes]
rs782615	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782617	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782618	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782620	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs782621	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs782623	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782624	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs782625	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782626	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782627	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782628	0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs782631	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782635	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782636	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782638	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782643	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782647	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782648	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs782651	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9636439	0.95[JPT][hapmap];0.87[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
rs782589	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	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
3	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:55826200-55842600	Weak transcription	Right Ventricle	heart
5	chr2:55826200-55843000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:55828200-55843600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:55829800-55842800	Weak transcription	Colonic Mucosa	Colon
8	chr2:55830400-55842800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:55830400-55843600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:55830400-55843600	Weak transcription	Aorta	Aorta
11	chr2:55832400-55842800	Weak transcription	Lung	lung
12	chr2:55835400-55842800	Weak transcription	Gastric	stomach
13	chr2:55836000-55842600	Weak transcription	Psoas Muscle	Psoas
14	chr2:55836000-55842600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:55836600-55843600	Weak transcription	Small Intestine	intestine
16	chr2:55836800-55842600	Weak transcription	Right Atrium	heart
17	chr2:55836800-55842800	Weak transcription	Left Ventricle	heart
18	chr2:55836800-55843600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:55837000-55842400	Weak transcription	Fetal Heart	heart
20	chr2:55837400-55842600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:55837400-55842600	Strong transcription	Fetal Thymus	thymus
22	chr2:55837600-55842200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:55837600-55842400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:55837600-55842400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr2:55837600-55842400	Strong transcription	HSMM	muscle
26	chr2:55837800-55842200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:55837800-55842400	Strong transcription	Placenta	Placenta
28	chr2:55837800-55842400	Strong transcription	Osteobl	bone
29	chr2:55837800-55842600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:55837800-55843400	Weak transcription	Stomach Mucosa	stomach
31	chr2:55838000-55842200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:55838000-55842200	Strong transcription	Adipose Nuclei	Adipose
33	chr2:55838000-55842400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:55838000-55842600	Strong transcription	Brain Germinal Matrix	brain
35	chr2:55838000-55843000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:55838200-55842200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:55838200-55842200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:55838200-55842600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:55838200-55842600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:55838200-55842600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:55838400-55842600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:55838400-55842600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:55838600-55842200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr2:55838600-55842600	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr2:55838800-55842200	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr2:55838800-55842800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:55839000-55842200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:55839000-55842400	Weak transcription	NHLF	lung
49	chr2:55839200-55842600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr2:55839200-55842800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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