Variant report

Variant	rs782573
Chromosome Location	chr2:55912961-55912962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55876589..55879257-chr2:55911121..55913801,2	K562	blood:
2	chr2:55912617..55915490-chr2:55920538..55922128,2	MCF-7	breast:
3	chr2:55911687..55914723-chr2:55917441..55920952,3	K562	blood:
4	chr2:55910858..55913187-chr2:55918020..55920146,2	K562	blood:
5	chr2:55906258..55908456-chr2:55912451..55914815,2	K562	blood:

Variant related genes	Relation type
ENSG00000138035	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10460508	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10496050	0.85[CEU][hapmap];0.86[YRI][hapmap]
rs1084522	0.85[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs1084525	0.96[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs12617719	0.83[AFR][1000 genomes]
rs17278044	0.86[CEU][hapmap];0.87[YRI][hapmap]
rs17369191	0.86[CEU][hapmap]
rs1823893	0.86[CEU][hapmap];0.87[YRI][hapmap]
rs1975484	0.86[CEU][hapmap]
rs1975487	0.85[CEU][hapmap]
rs2586950	0.87[YRI][hapmap]
rs2586954	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2586969	0.91[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap]
rs2586970	0.91[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap]
rs2627765	0.92[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2627766	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2627767	0.80[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2627769	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2627772	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2627773	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627775	0.83[JPT][hapmap];0.86[YRI][hapmap]
rs2627776	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs2627779	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35504023	0.85[CEU][hapmap];0.86[YRI][hapmap]
rs4290693	0.85[CEU][hapmap];0.86[YRI][hapmap]
rs4312532	0.83[YRI][hapmap]
rs62165255	0.83[AMR][1000 genomes]
rs6545506	0.85[CEU][hapmap];0.86[YRI][hapmap]
rs706548	0.83[JPT][hapmap]
rs7582278	0.87[YRI][hapmap]
rs7589673	0.81[EUR][1000 genomes]
rs782566	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782567	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs782568	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782579	0.88[ASN][1000 genomes]
rs782584	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs782585	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs782586	0.85[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs782588	0.85[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs782590	0.81[CEU][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs782595	0.86[CEU][hapmap];0.87[YRI][hapmap]
rs782599	0.87[YRI][hapmap]
rs782602	0.83[JPT][hapmap];0.86[YRI][hapmap]
rs782606	0.89[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs782619	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782622	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782629	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782630	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782632	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs782633	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782634	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs782637	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782641	0.85[AMR][1000 genomes]
rs782642	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs782644	0.81[AMR][1000 genomes]
rs782652	0.89[CEU][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap]
rs809732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs935177	0.82[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv9802	chr2:55910254-55939253	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv16137	chr2:55910848-55938746	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	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
rs782573	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
3	chr2:55864400-55919600	Weak transcription	NHLF	lung
4	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
8	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
9	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
10	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
11	chr2:55879000-55917600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:55879400-55914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:55881200-55913000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:55883000-55919800	Weak transcription	HSMMtube	muscle
15	chr2:55889800-55918400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:55890200-55915600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:55890400-55914200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:55892000-55914000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:55892200-55914000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:55892400-55919800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:55892600-55917000	Strong transcription	Dnd41	blood
22	chr2:55893200-55915800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:55894000-55919800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:55895800-55920000	Weak transcription	Right Ventricle	heart
25	chr2:55897000-55914400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:55897600-55913600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:55897600-55914200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:55898000-55913600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:55901200-55915000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:55901200-55915200	Strong transcription	GM12878-XiMat	blood
31	chr2:55901800-55914200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:55901800-55916000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:55902000-55914000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:55902000-55914000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr2:55902000-55915200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:55902000-55916000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:55903200-55915800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:55903400-55914200	Strong transcription	Adipose Nuclei	Adipose
39	chr2:55903600-55913200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:55903600-55914200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:55903600-55915800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:55904000-55913400	Strong transcription	Fetal Thymus	thymus
43	chr2:55904000-55913800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:55904000-55914000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:55904000-55914200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:55904200-55916400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:55904200-55920600	Weak transcription	Stomach Mucosa	stomach
48	chr2:55904600-55920200	Weak transcription	Gastric	stomach
49	chr2:55905000-55913800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr2:55905000-55913800	Strong transcription	Brain Anterior Caudate	brain

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