Variant report

Variant	rs62165178
Chromosome Location	chr2:55755166-55755167
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	MAFF	chr2:55755164-55755329	HepG2	liver:	n/a	chr2:55755206-55755224
2	MAFK	chr2:55755107-55755368	HepG2	liver:	n/a	chr2:55755208-55755223
3	MAFK	chr2:55755137-55755296	HepG2	liver:	n/a	chr2:55755208-55755223

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55754380..55757181-chr2:55762794..55765251,2	K562	blood:

Variant related genes	Relation type
CCDC104	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1037508	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1045910	0.86[ASN][1000 genomes]
rs1045920	0.90[AFR][1000 genomes]
rs12463766	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12619756	0.87[ASN][1000 genomes]
rs12989898	0.91[ASN][1000 genomes]
rs13016772	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs13028892	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13403782	0.83[EUR][1000 genomes]
rs1563201	0.84[ASN][1000 genomes]
rs2168097	0.84[ASN][1000 genomes]
rs2586946	0.83[ASN][1000 genomes]
rs2586948	0.83[ASN][1000 genomes]
rs2586965	0.84[ASN][1000 genomes]
rs2627758	0.84[ASN][1000 genomes]
rs2627763	0.84[ASN][1000 genomes]
rs2627783	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3748945	0.96[ASN][1000 genomes]
rs3816489	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4233962	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671248	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545505	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6716100	0.84[AFR][1000 genomes]
rs6717574	0.82[AFR][1000 genomes]
rs6731927	0.84[ASN][1000 genomes]
rs730884	0.91[ASN][1000 genomes]
rs744514	0.91[ASN][1000 genomes]
rs7571482	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7574398	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7585484	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7586124	0.86[AFR][1000 genomes]
rs7605486	0.84[ASN][1000 genomes]
rs7605504	0.84[ASN][1000 genomes]
rs782589	0.82[ASN][1000 genomes]
rs782591	0.83[ASN][1000 genomes]
rs782593	0.83[ASN][1000 genomes]
rs782597	0.80[ASN][1000 genomes]
rs782598	0.83[ASN][1000 genomes]
rs782603	0.82[ASN][1000 genomes]
rs782612	0.84[ASN][1000 genomes]
rs782648	0.80[ASN][1000 genomes]
rs782651	0.80[ASN][1000 genomes]
rs9636439	0.90[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
rs62165178	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
2	chr2:55748000-55757600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:55748000-55761200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:55748000-55761200	Weak transcription	Primary B cells from cord blood	blood
5	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
7	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
8	chr2:55748200-55756600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:55748200-55757200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:55748200-55757200	Weak transcription	Brain Angular Gyrus	brain
11	chr2:55748200-55757200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:55748200-55757400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:55748200-55764600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:55748200-55764600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:55748200-55765000	Weak transcription	K562	blood
16	chr2:55748200-55769600	Weak transcription	Small Intestine	intestine
17	chr2:55748200-55769600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:55748200-55772000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:55748200-55773000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:55748200-55775800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:55748200-55777400	Weak transcription	NHLF	lung
22	chr2:55748200-55778800	Weak transcription	Fetal Heart	heart
23	chr2:55748200-55782400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:55748400-55761400	Weak transcription	NHEK	skin
25	chr2:55748400-55764400	Weak transcription	GM12878-XiMat	blood
26	chr2:55748400-55772200	Weak transcription	HMEC	breast
27	chr2:55748600-55770000	Weak transcription	Dnd41	blood
28	chr2:55749400-55758600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:55749600-55758800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:55749600-55760000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:55749800-55756800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr2:55750000-55775400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:55750400-55760400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:55750600-55755400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:55750600-55760200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:55750800-55759400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:55751000-55755200	Strong transcription	Fetal Brain Female	brain
38	chr2:55751000-55755200	Strong transcription	Fetal Lung	lung
39	chr2:55751000-55759200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:55751000-55759200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:55751000-55759200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:55751200-55758200	Strong transcription	Fetal Intestine Small	intestine
43	chr2:55751200-55759400	Strong transcription	Fetal Stomach	stomach
44	chr2:55751400-55756200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:55751400-55764200	Weak transcription	HSMM	muscle
46	chr2:55751600-55757400	Weak transcription	HUVEC	blood vessel
47	chr2:55751800-55757400	Weak transcription	NH-A	brain
48	chr2:55751800-55766600	Weak transcription	Liver	Liver
49	chr2:55752200-55755800	Strong transcription	Ovary	ovary
50	chr2:55752400-55756800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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