Variant report

Variant	rs2586950
Chromosome Location	chr2:55868966-55868967
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55867632..55869380-chr2:55872094..55873711,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10460508	0.81[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10496050	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1084522	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1084525	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12329050	0.87[YRI][hapmap]
rs17278044	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17369191	0.91[JPT][hapmap];0.87[YRI][hapmap]
rs1823893	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1975484	0.82[JPT][hapmap]
rs1975487	0.91[JPT][hapmap];0.86[YRI][hapmap]
rs2586947	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2586952	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2586954	0.81[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2586968	0.82[AFR][1000 genomes]
rs2586969	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2586970	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2627759	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2627765	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2627766	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2627772	0.83[AFR][1000 genomes]
rs2627773	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2627775	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2627776	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2627777	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2627779	0.85[AFR][1000 genomes]
rs2627780	0.80[AFR][1000 genomes]
rs2627782	0.82[AFR][1000 genomes]
rs35504023	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4290693	0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4312532	0.96[YRI][hapmap]
rs4672056	0.82[AFR][1000 genomes]
rs58003472	0.82[AFR][1000 genomes]
rs6545506	0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs706548	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7582278	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7596377	0.88[YRI][hapmap]
rs782566	0.88[AFR][1000 genomes]
rs782567	0.89[AFR][1000 genomes]
rs782568	0.81[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs782572	0.88[YRI][hapmap]
rs782573	0.87[YRI][hapmap]
rs782584	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs782586	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs782587	0.88[ASN][1000 genomes]
rs782588	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs782590	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs782594	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs782595	1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs782599	0.88[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs782600	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs782601	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs782602	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs782606	0.81[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs782629	0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs782630	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs782632	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs782633	0.82[AFR][1000 genomes]
rs782634	0.81[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs782637	0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs782649	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs782650	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs782652	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs809732	0.88[YRI][hapmap]
rs935177	1.00[YRI][hapmap];0.82[AFR][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
rs2586950	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	chr2:55849200-55869400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:55849200-55873200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:55849800-55869400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:55849800-55882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:55851400-55870000	Weak transcription	Spleen	Spleen
15	chr2:55852000-55872400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:55853600-55882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:55857000-55873800	Strong transcription	Fetal Thymus	thymus
18	chr2:55857600-55869800	Weak transcription	Brain Angular Gyrus	brain
19	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
20	chr2:55858600-55871600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:55858800-55873400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:55858800-55875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:55858800-55877200	Strong transcription	Dnd41	blood
24	chr2:55859000-55876800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:55859000-55877000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:55859000-55877200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:55859200-55874000	Weak transcription	Pancreas	Pancrea
28	chr2:55859400-55875600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:55859400-55877600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:55859800-55871200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:55859800-55871400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:55859800-55873200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:55859800-55873600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
35	chr2:55860600-55869800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr2:55860800-55871200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:55861800-55875000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:55861800-55875800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr2:55862000-55873400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:55862000-55874800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr2:55862000-55875000	Strong transcription	Fetal Intestine Large	intestine
42	chr2:55862000-55877200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:55862000-55877800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:55862200-55871200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:55862200-55871200	Strong transcription	A549	lung
46	chr2:55862200-55871400	Strong transcription	GM12878-XiMat	blood
47	chr2:55862200-55873800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:55862200-55874000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:55862200-55874400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:55862200-55874800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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