Variant report

Variant	rs782588
Chromosome Location	chr2:55841640-55841641
allele	C/T
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	chr2:55841514-55841656	K562	blood:	n/a	n/a
2	POLR2A	chr2:55841593-55846281	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55645913..55647717-chr2:55840630..55843041,2	K562	blood:

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

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10165864	0.85[CEU][hapmap]
rs10454749	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10460508	0.96[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs10496050	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1058582	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1084522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1084525	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11125579	0.83[EUR][1000 genomes]
rs11125581	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12329050	0.90[YRI][hapmap]
rs17278044	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17369191	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17798852	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1823893	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1975484	1.00[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1975487	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2586947	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2586950	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2586954	0.96[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs2586968	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2586969	0.85[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2586970	0.85[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2627759	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627765	0.82[CEU][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap]
rs2627773	0.81[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs2627775	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2627776	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2627777	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2627780	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2627782	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35504023	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3762513	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4290693	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4312532	0.95[YRI][hapmap]
rs4672052	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4672054	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4672055	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4672056	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55761024	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58003472	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62165173	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62165181	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62165182	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165183	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165184	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62165196	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62165197	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62165200	0.82[AFR][1000 genomes]
rs6545506	1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6739513	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs706548	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs7582278	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7594279	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7596377	0.91[YRI][hapmap]
rs7598650	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs782568	0.96[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs782572	0.85[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs782573	0.85[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs782584	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap]
rs782586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782587	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782590	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782594	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782595	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782599	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782600	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782601	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782602	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782606	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs782629	0.81[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs782630	0.83[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs782632	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs782634	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs782637	0.94[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs782649	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782650	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782652	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs809732	0.85[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs935177	0.85[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9917139	0.85[CEU][hapmap]

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	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
4	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
5	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
6	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
7	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs782588	PNPT1	cis	cerebellum	SCAN
rs782588	PNPT1	Cis_1M	lymphoblastoid	RTeQTL
rs782588	CCDC104	cis	parietal	SCAN
rs782588	SMEK2	cis	parietal	SCAN
rs782588	PNPT1	cis	lymphoblastoid	seeQTL

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	chr2:55837400-55842000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:55837400-55842600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:55837400-55842600	Strong transcription	Fetal Thymus	thymus
23	chr2:55837600-55842000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:55837600-55842200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:55837600-55842400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:55837600-55842400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:55837600-55842400	Strong transcription	HSMM	muscle
28	chr2:55837800-55842000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:55837800-55842200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:55837800-55842400	Strong transcription	Placenta	Placenta
31	chr2:55837800-55842400	Strong transcription	Osteobl	bone
32	chr2:55837800-55842600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:55837800-55843400	Weak transcription	Stomach Mucosa	stomach
34	chr2:55838000-55842200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:55838000-55842200	Strong transcription	Adipose Nuclei	Adipose
36	chr2:55838000-55842400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:55838000-55842600	Strong transcription	Brain Germinal Matrix	brain
38	chr2:55838000-55843000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:55838200-55842200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:55838200-55842200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:55838200-55842600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:55838200-55842600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:55838200-55842600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:55838400-55842000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:55838400-55842000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:55838400-55842000	Strong transcription	Brain Anterior Caudate	brain
47	chr2:55838400-55842000	Strong transcription	HMEC	breast
48	chr2:55838400-55842600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:55838400-55842600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr2:55838600-55841800	Strong transcription	Liver	Liver

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