Variant report

Variant	rs4788553
Chromosome Location	chr16:71780277-71780278
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71758014..71760790-chr16:71779924..71782486,2	K562	blood:
2	chr16:71779409..71781873-chr16:71787219..71789998,2	K562	blood:
3	chr16:71770040..71772429-chr16:71777706..71780702,2	MCF-7	breast:
4	chr16:71779212..71782011-chr16:71841808..71844042,2	MCF-7	breast:
5	chr16:71598892..71599509-chr16:71780071..71780629,2	MCF-7	breast:
6	chr16:71598713..71599448-chr16:71780084..71781049,2	K562	blood:

Variant related genes	Relation type
ENSG00000040199	Chromatin interaction
ENSG00000157429	Chromatin interaction
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1058750	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852502	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852503	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075893	0.85[EUR][1000 genomes]
rs11075894	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075898	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075901	0.82[EUR][1000 genomes]
rs11075904	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075905	0.85[EUR][1000 genomes]
rs11862723	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12923990	0.89[EUR][1000 genomes]
rs12929547	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364210	1.00[ASN][1000 genomes]
rs1392484	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423983	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032918	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052584	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052585	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113223	1.00[ASN][1000 genomes]
rs2133773	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247603	1.00[ASN][1000 genomes]
rs2334877	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2334880	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4354946	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788548	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788550	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788557	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788559	0.85[EUR][1000 genomes]
rs4788810	1.00[ASN][1000 genomes]
rs4788813	1.00[ASN][1000 genomes]
rs4788820	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788822	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788823	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788825	0.85[EUR][1000 genomes]
rs4788828	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788830	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499526	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499527	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499528	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499529	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499530	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499531	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499534	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499538	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499540	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186112	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187948	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188675	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190487	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193549	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195059	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201649	0.86[EUR][1000 genomes]
rs7201712	0.82[EUR][1000 genomes]
rs7202479	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204118	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7204608	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204967	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204992	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206470	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7359478	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044144	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8051968	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052910	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053186	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053745	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055419	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8058297	0.87[EUR][1000 genomes]
rs8062188	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889568	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302630	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs9635524	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979790	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888756	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929840	0.94[EUR][1000 genomes]
rs9929985	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930015	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9931074	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934301	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934715	0.85[AFR][1000 genomes]
rs9937511	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939458	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv1817133	chr16:71705908-71837477	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS 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	89 gene(s)	inside rSNPs	diseases
4	esv1819402	chr16:71755852-71816899	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4788553	MARVELD3	cis	Skin Sun Exposed Lower leg	GTEx
rs4788553	PHLPP2	cis	Muscle Skeletal	GTEx
rs4788553	PHLPP2	cis	Artery Aorta	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71761000-71805600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:71762200-71811400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:71763200-71799800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr16:71763200-71812600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr16:71763400-71802200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr16:71763600-71784400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr16:71763600-71786200	Strong transcription	Osteobl	bone
8	chr16:71763600-71793000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr16:71763600-71800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr16:71763600-71801400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr16:71763600-71812400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:71763800-71799600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr16:71763800-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr16:71764000-71784200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr16:71764000-71785200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:71764000-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr16:71764000-71813000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr16:71764200-71784400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr16:71764400-71782000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr16:71764400-71784400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr16:71764400-71784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:71764600-71784600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr16:71764800-71802600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr16:71765600-71785200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr16:71767000-71784600	Strong transcription	Fetal Muscle Leg	muscle
26	chr16:71767000-71787400	Weak transcription	Stomach Mucosa	stomach
27	chr16:71769000-71783200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr16:71770400-71785600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:71770600-71784400	Strong transcription	Adipose Nuclei	Adipose
30	chr16:71770600-71784600	Strong transcription	Fetal Thymus	thymus
31	chr16:71770600-71793000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr16:71770600-71796000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr16:71770600-71798600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr16:71770600-71799600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr16:71770800-71782400	Strong transcription	HUVEC	blood vessel
36	chr16:71770800-71784200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr16:71770800-71784200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr16:71770800-71793200	Strong transcription	HSMM	muscle
39	chr16:71770800-71793600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr16:71770800-71795800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr16:71770800-71799600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr16:71770800-71810600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr16:71770800-71813800	Strong transcription	Liver	Liver
44	chr16:71771000-71784400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr16:71771000-71784400	Strong transcription	Fetal Lung	lung
46	chr16:71771000-71793200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr16:71771000-71812200	Strong transcription	Placenta	Placenta
48	chr16:71771400-71784200	Strong transcription	NHDF-Ad	bronchial
49	chr16:71772400-71783000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr16:71773200-71786600	Weak transcription	Fetal Brain Male	brain

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