Variant report

Variant	rs6739513
Chromosome Location	chr2:55749902-55749903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55749760..55752238-chr2:55760020..55761976,2	K562	blood:
2	chr2:55742826..55746774-chr2:55749245..55752700,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163001	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10165864	0.80[EUR][1000 genomes]
rs10181648	0.81[EUR][1000 genomes]
rs10454749	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10496050	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1058582	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1084522	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11125579	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11125581	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17278044	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17369191	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17798852	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1823893	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1975484	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1975487	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2586947	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2586968	0.89[AFR][1000 genomes]
rs2586969	0.89[AFR][1000 genomes]
rs2586970	0.89[AFR][1000 genomes]
rs2627759	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2627780	0.84[AFR][1000 genomes]
rs2627782	0.89[AFR][1000 genomes]
rs35504023	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3762513	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4290693	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4672052	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4672054	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4672055	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4672056	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55761024	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58003472	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62165173	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62165181	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62165182	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165183	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62165184	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62165196	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165197	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62165200	0.85[AFR][1000 genomes]
rs6545506	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7582278	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7594279	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7598650	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs782586	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs782587	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs782588	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs782590	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs782594	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs782595	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs782599	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs782600	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs782601	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs782602	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs782649	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs782650	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs935177	0.89[AFR][1000 genomes]
rs9917139	0.81[EUR][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
rs6739513	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	chr2:55747600-55752200	Weak transcription	Lung	lung
2	chr2:55747600-55753000	Weak transcription	Spleen	Spleen
3	chr2:55747800-55751000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:55747800-55751200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:55747800-55751400	Weak transcription	Pancreas	Pancrea
6	chr2:55747800-55752000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:55747800-55752800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:55747800-55753600	Weak transcription	Gastric	stomach
9	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
10	chr2:55748000-55750000	Weak transcription	Left Ventricle	heart
11	chr2:55748000-55751400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:55748000-55751600	Weak transcription	Liver	Liver
13	chr2:55748000-55752000	Weak transcription	Stomach Mucosa	stomach
14	chr2:55748000-55752200	Weak transcription	Placenta	Placenta
15	chr2:55748000-55752200	Weak transcription	Ovary	ovary
16	chr2:55748000-55752200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:55748000-55752200	Weak transcription	Right Ventricle	heart
18	chr2:55748000-55752400	Weak transcription	Aorta	Aorta
19	chr2:55748000-55753000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:55748000-55757600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:55748000-55761200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:55748000-55761200	Weak transcription	Primary B cells from cord blood	blood
23	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
25	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
26	chr2:55748200-55750600	Weak transcription	HUVEC	blood vessel
27	chr2:55748200-55750600	Weak transcription	NH-A	brain
28	chr2:55748200-55750800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:55748200-55750800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:55748200-55750800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:55748200-55750800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:55748200-55750800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:55748200-55750800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:55748200-55750800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:55748200-55750800	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:55748200-55750800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:55748200-55750800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:55748200-55750800	Weak transcription	Fetal Thymus	thymus
39	chr2:55748200-55750800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:55748200-55750800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:55748200-55750800	Weak transcription	HSMM	muscle
42	chr2:55748200-55750800	Weak transcription	NHDF-Ad	bronchial
43	chr2:55748200-55751000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:55748200-55751000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:55748200-55751000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:55748200-55751000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:55748200-55751000	Weak transcription	Fetal Brain Female	brain
48	chr2:55748200-55751000	Weak transcription	Fetal Lung	lung
49	chr2:55748200-55751200	Weak transcription	Primary T cells from cord blood	blood
50	chr2:55748200-55751200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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