Variant report

Variant	rs1045910
Chromosome Location	chr2:55771161-55771162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1037508	0.86[ASN][1000 genomes]
rs10427222	0.81[JPT][hapmap]
rs11900763	0.81[JPT][hapmap]
rs12463766	0.85[ASN][1000 genomes]
rs12617829	0.85[CHB][hapmap]
rs12619756	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12713301	0.92[EUR][1000 genomes]
rs12989898	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs13016772	0.87[ASN][1000 genomes]
rs13028892	0.85[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs13427693	0.92[EUR][1000 genomes]
rs13430657	0.92[EUR][1000 genomes]
rs1373228	0.85[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1563201	0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1814457	0.88[ASN][1000 genomes]
rs1975485	0.85[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1975486	0.85[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2168097	0.96[ASN][1000 genomes]
rs2586946	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2586948	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2586949	1.00[ASW][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2586951	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2586955	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2586958	0.90[EUR][1000 genomes]
rs2586959	0.92[EUR][1000 genomes]
rs2586960	0.92[EUR][1000 genomes]
rs2586961	0.92[EUR][1000 genomes]
rs2586965	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627758	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627763	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627768	0.82[EUR][1000 genomes]
rs2627774	0.92[EUR][1000 genomes]
rs2627778	0.91[CHB][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2627781	0.90[EUR][1000 genomes]
rs2627783	0.84[ASN][1000 genomes]
rs3748945	0.87[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs3816489	0.87[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4233962	0.86[ASN][1000 genomes]
rs4671248	0.87[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs61475257	0.92[ASN][1000 genomes]
rs62165178	0.86[ASN][1000 genomes]
rs6545503	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6545505	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6716100	0.86[JPT][hapmap]
rs6731927	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs706549	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs706550	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs706551	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs730884	0.84[ASN][1000 genomes]
rs744514	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7559307	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7585484	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7605486	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7605504	0.97[ASN][1000 genomes]
rs782569	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782570	0.92[EUR][1000 genomes]
rs782571	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs782574	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs782575	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs782576	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782577	0.92[EUR][1000 genomes]
rs782580	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs782582	0.92[EUR][1000 genomes]
rs782583	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs782589	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]
rs782591	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782593	1.00[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782597	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs782598	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782603	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs782604	0.85[CEU][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782612	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782614	0.83[ASN][1000 genomes]
rs782615	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs782617	0.92[EUR][1000 genomes]
rs782618	0.82[EUR][1000 genomes]
rs782620	1.00[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs782621	0.85[CEU][hapmap];0.81[CHB][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs782623	0.90[EUR][1000 genomes]
rs782624	0.92[EUR][1000 genomes]
rs782625	0.92[EUR][1000 genomes]
rs782626	0.92[EUR][1000 genomes]
rs782627	0.92[EUR][1000 genomes]
rs782628	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs782631	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782635	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782636	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782638	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782643	0.86[EUR][1000 genomes]
rs782647	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs782648	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs782651	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9636439	0.82[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1045910	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
2	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
4	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
5	chr2:55748200-55772000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:55748200-55773000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:55748200-55775800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:55748200-55777400	Weak transcription	NHLF	lung
9	chr2:55748200-55778800	Weak transcription	Fetal Heart	heart
10	chr2:55748200-55782400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:55748400-55772200	Weak transcription	HMEC	breast
12	chr2:55750000-55775400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:55752600-55788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
15	chr2:55753200-55772400	Weak transcription	HepG2	liver
16	chr2:55753400-55772200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:55753600-55786600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:55754000-55774600	Weak transcription	Spleen	Spleen
19	chr2:55754000-55784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:55754200-55772400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:55754400-55772200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:55754400-55783000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:55758000-55771400	Weak transcription	NH-A	brain
24	chr2:55758200-55781200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:55758200-55783800	Weak transcription	Gastric	stomach
26	chr2:55758200-55784000	Weak transcription	Pancreas	Pancrea
27	chr2:55758400-55774000	Weak transcription	Hela-S3	cervix
28	chr2:55758400-55776000	Weak transcription	HUVEC	blood vessel
29	chr2:55758600-55784000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:55759200-55772400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:55759600-55773800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:55760800-55788000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:55761000-55788200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:55761200-55777200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:55761400-55781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:55762000-55772200	Weak transcription	Brain Germinal Matrix	brain
37	chr2:55762000-55783800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:55762200-55771200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:55762200-55771200	Weak transcription	Lung	lung
40	chr2:55762200-55771800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:55762200-55773000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:55762200-55782600	Weak transcription	NHEK	skin
43	chr2:55762200-55784000	Weak transcription	Right Ventricle	heart
44	chr2:55762800-55781000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:55763000-55771600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:55763800-55773600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:55764400-55771400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:55765000-55771200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:55765000-55771200	Weak transcription	Ovary	ovary
50	chr2:55765000-55771200	Weak transcription	Thymus	Thymus

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