Variant report

Variant	rs782601
Chromosome Location	chr2:55848244-55848245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55847510-55848770	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:55848173-55849329	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
2	chr2:55818262..55820533-chr2:55847496..55849858,2	MCF-7	breast:
3	chr2:55843280..55846696-chr2:55847912..55852861,6	MCF-7	breast:
4	chr2:55847894..55850021-chr2:55856235..55857780,2	MCF-7	breast:
5	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:

No data

Variant related genes	Relation type
SMEK2	TF binding region
ENSG00000138041	Chromatin interaction
ENSG00000115355	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10454749	0.80[AMR][1000 genomes]
rs10460508	0.81[AFR][1000 genomes]
rs10496050	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1058582	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1084522	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125581	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17278044	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17369191	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17798852	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1823893	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1975484	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1975487	0.83[EUR][1000 genomes]
rs2054728	0.83[AFR][1000 genomes]
rs2586947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2586950	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2586968	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2586969	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2586970	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2627759	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627775	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2627776	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2627777	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2627780	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2627782	0.97[AFR][1000 genomes]
rs35504023	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3762513	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4290693	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4672052	0.80[EUR][1000 genomes]
rs4672054	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4672055	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4672056	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55761024	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58003472	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62165173	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62165181	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62165182	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62165183	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62165184	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62165196	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62165197	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165200	0.93[AFR][1000 genomes]
rs6545506	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6739513	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6744213	0.83[AFR][1000 genomes]
rs706548	0.95[ASN][1000 genomes]
rs7582278	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7594279	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7598650	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs782566	0.80[AFR][1000 genomes]
rs782567	0.81[AFR][1000 genomes]
rs782568	0.81[AFR][1000 genomes]
rs782586	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782587	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782588	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782590	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782594	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782595	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782613	0.84[AFR][1000 genomes]
rs782649	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782650	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782652	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935177	0.97[AFR][1000 genomes];0.81[AMR][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
rs782601	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:55846600-55848600	Weak transcription	Esophagus	oesophagus
4	chr2:55846600-55848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:55846600-55849000	Enhancers	Colon Smooth Muscle	Colon
6	chr2:55846600-55850400	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr2:55846600-55851600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:55846600-55852000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:55846600-55859400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:55846600-55861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:55846600-55862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
14	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:55846800-55848400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:55846800-55848600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:55846800-55848600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:55846800-55848600	Weak transcription	Fetal Brain Female	brain
20	chr2:55846800-55848800	Enhancers	Adipose Nuclei	Adipose
21	chr2:55846800-55848800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:55846800-55848800	Enhancers	Pancreas	Pancrea
23	chr2:55846800-55850400	Enhancers	Liver	Liver
24	chr2:55846800-55851200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr2:55846800-55853000	Weak transcription	A549	lung
26	chr2:55846800-55858200	Weak transcription	HSMM	muscle
27	chr2:55846800-55862000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:55846800-55862000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:55846800-55862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:55846800-55862600	Weak transcription	NHDF-Ad	bronchial
31	chr2:55846800-55863400	Weak transcription	HSMMtube	muscle
32	chr2:55846800-55863400	Weak transcription	NHLF	lung
33	chr2:55846800-55863800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:55847000-55849400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:55847000-55852600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr2:55847200-55849200	Weak transcription	Ovary	ovary
38	chr2:55847400-55848400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:55847400-55848600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:55847400-55848800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:55847400-55849200	Genic enhancers	Lung	lung
42	chr2:55847400-55852400	Weak transcription	HMEC	breast
43	chr2:55847400-55852800	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr2:55847400-55859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:55847400-55862200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:55847600-55848400	Weak transcription	Fetal Lung	lung
48	chr2:55847600-55848400	Weak transcription	Placenta	Placenta
49	chr2:55847600-55848600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:55847600-55848600	Enhancers	Primary T cells from cord blood	blood

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