Variant report

Variant	rs28710456
Chromosome Location	chr4:152667171-152667172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:152664924..152667297-chr4:152847686..152849611,2	K562	blood:
2	chr4:152661963..152664459-chr4:152666198..152669566,3	K562	blood:
3	chr4:152664298..152671404-chr4:152680286..152684631,9	K562	blood:
4	chr4:152661372..152664044-chr4:152665414..152668096,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000059691	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10007015	0.87[EUR][1000 genomes]
rs10007167	0.87[EUR][1000 genomes]
rs10019048	0.87[EUR][1000 genomes]
rs10023298	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028410	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10028961	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049728	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049991	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10776524	0.87[EUR][1000 genomes]
rs1105534	0.87[EUR][1000 genomes]
rs1105535	0.87[EUR][1000 genomes]
rs1105536	0.87[EUR][1000 genomes]
rs11734799	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11932383	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12331037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502055	0.87[EUR][1000 genomes]
rs13137669	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13138986	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13146981	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13149588	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1355413	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1366909	0.87[EUR][1000 genomes]
rs1511170	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17027798	0.86[EUR][1000 genomes]
rs17360475	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1877187	0.87[EUR][1000 genomes]
rs1896883	0.86[EUR][1000 genomes]
rs2007218	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2007445	0.87[EUR][1000 genomes]
rs2303866	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2840130	0.87[EUR][1000 genomes]
rs28637056	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749561	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3749563	0.86[EUR][1000 genomes]
rs3792691	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4383600	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4571	0.86[EUR][1000 genomes]
rs4696104	0.87[EUR][1000 genomes]
rs4696109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696111	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696277	0.82[EUR][1000 genomes]
rs4696283	0.85[EUR][1000 genomes]
rs4696284	0.87[EUR][1000 genomes]
rs4696285	0.87[EUR][1000 genomes]
rs4696291	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696293	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696294	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62327352	0.86[AMR][1000 genomes]
rs6535809	0.87[EUR][1000 genomes]
rs6535811	0.87[EUR][1000 genomes]
rs6535812	0.87[EUR][1000 genomes]
rs6535813	0.86[EUR][1000 genomes]
rs6535814	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6535815	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6535817	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6535818	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6535819	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6535821	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6810860	0.87[EUR][1000 genomes]
rs6817058	0.87[EUR][1000 genomes]
rs6817586	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6818667	0.87[EUR][1000 genomes]
rs6823002	0.87[EUR][1000 genomes]
rs6823194	0.87[EUR][1000 genomes]
rs6823421	0.87[EUR][1000 genomes]
rs6823423	0.87[EUR][1000 genomes]
rs6823462	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6832562	0.87[EUR][1000 genomes]
rs6833368	0.87[EUR][1000 genomes]
rs6834095	0.87[EUR][1000 genomes]
rs6838966	0.87[EUR][1000 genomes]
rs6839074	0.87[EUR][1000 genomes]
rs6840360	0.87[EUR][1000 genomes]
rs6840678	0.87[EUR][1000 genomes]
rs6841204	0.87[EUR][1000 genomes]
rs6841783	0.87[EUR][1000 genomes]
rs6845944	0.86[EUR][1000 genomes]
rs6846114	0.87[EUR][1000 genomes]
rs6849050	0.87[EUR][1000 genomes]
rs7439465	0.86[EUR][1000 genomes]
rs749982	0.87[EUR][1000 genomes]
rs751012	0.87[EUR][1000 genomes]
rs751014	0.87[EUR][1000 genomes]
rs7663045	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7667197	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7669977	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7671651	0.86[EUR][1000 genomes]
rs7684350	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695162	0.81[EUR][1000 genomes]
rs907237	0.87[EUR][1000 genomes]
rs9307887	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995704	0.83[EUR][1000 genomes]
rs9998462	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508322	chr4:152617079-152678951	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28710456	PET112L	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152629200-152681400	Weak transcription	Colonic Mucosa	Colon
2	chr4:152629400-152681200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:152651800-152667200	Weak transcription	Gastric	stomach
4	chr4:152651800-152681400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:152657800-152674000	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:152657800-152677600	Weak transcription	Brain Anterior Caudate	brain
7	chr4:152658200-152667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:152658400-152674200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:152658600-152674000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:152658600-152681200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:152659000-152674000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:152659000-152681400	Weak transcription	Pancreas	Pancrea
13	chr4:152659200-152673800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:152659200-152674200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:152659200-152674400	Weak transcription	Right Ventricle	heart
16	chr4:152659400-152668200	Weak transcription	HepG2	liver
17	chr4:152659400-152674000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:152659400-152674200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:152659400-152674600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:152659400-152675200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:152659400-152675400	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:152659400-152677200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:152659400-152678400	Weak transcription	Fetal Stomach	stomach
24	chr4:152659400-152681400	Weak transcription	Thymus	Thymus
25	chr4:152659600-152668000	Weak transcription	Lung	lung
26	chr4:152659600-152668400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:152659600-152673800	Weak transcription	Fetal Thymus	thymus
28	chr4:152659600-152674200	Weak transcription	Aorta	Aorta
29	chr4:152659600-152674800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr4:152659600-152681200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:152659800-152681400	Weak transcription	Spleen	Spleen
32	chr4:152660000-152674200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:152660200-152674200	Weak transcription	Esophagus	oesophagus
34	chr4:152660600-152673800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:152660800-152667200	Weak transcription	Right Atrium	heart
36	chr4:152660800-152667200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:152660800-152671400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr4:152660800-152674200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:152660800-152675000	Weak transcription	Left Ventricle	heart
40	chr4:152660800-152681000	Weak transcription	Fetal Lung	lung
41	chr4:152661000-152667200	Weak transcription	Psoas Muscle	Psoas
42	chr4:152661200-152670800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:152661600-152674200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr4:152661600-152674800	Weak transcription	Dnd41	blood
45	chr4:152661800-152672200	Weak transcription	Primary B cells from cord blood	blood
46	chr4:152662000-152667600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:152662400-152671000	Weak transcription	Liver	Liver
48	chr4:152662600-152681400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr4:152663000-152671200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:152663000-152671200	Weak transcription	Monocytes-CD14+_RO01746	blood

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