Variant report

Variant	rs4788823
Chromosome Location	chr16:71688055-71688056
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	chr16:71686286..71688499-chr16:71756358..71758868,2	MCF-7	breast:
2	chr16:71686341..71688675-chr16:71691645..71694009,2	K562	blood:

Variant related genes	Relation type
ENSG00000261513	Chromatin interaction
ENSG00000040199	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1058750	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852502	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852503	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075893	0.94[EUR][1000 genomes]
rs11075894	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075898	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075904	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862723	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12923990	0.87[EUR][1000 genomes]
rs12929547	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364210	1.00[ASN][1000 genomes]
rs1392484	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423983	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032918	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052584	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052585	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113223	1.00[ASN][1000 genomes]
rs2133773	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247603	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2334877	0.81[EUR][1000 genomes]
rs2334880	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4354946	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788548	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788550	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788553	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788557	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788810	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788813	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788820	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788822	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788825	0.92[EUR][1000 genomes]
rs4788828	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788830	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499526	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499527	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499528	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499529	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499530	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499531	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499534	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499538	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499540	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186112	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187948	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188675	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190487	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193549	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195059	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201649	0.82[EUR][1000 genomes]
rs7202479	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204118	0.83[EUR][1000 genomes]
rs7204608	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204967	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204992	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206470	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7359478	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044144	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8051968	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052910	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053186	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055419	0.84[EUR][1000 genomes]
rs8058297	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8062188	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889568	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9635524	1.00[ASN][1000 genomes]
rs979790	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888756	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929840	0.85[EUR][1000 genomes]
rs9929985	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930015	0.84[EUR][1000 genomes]
rs9931074	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934301	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934789	0.88[EUR][1000 genomes]
rs9937511	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939458	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv962218	chr16:71645202-71727606	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4788823	MARVELD3	cis	Skin Sun Exposed Lower leg	GTEx
rs4788823	PHLPP2	cis	Artery Aorta	GTEx
rs4788823	PHLPP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71668000-71703000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr16:71671800-71704000	Weak transcription	Fetal Brain Male	brain
3	chr16:71672000-71741400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:71674800-71704600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr16:71675000-71724000	Weak transcription	Esophagus	oesophagus
6	chr16:71676800-71692200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr16:71676800-71693600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr16:71677800-71688800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr16:71679000-71693000	Strong transcription	HSMM	muscle
10	chr16:71679200-71693000	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr16:71681000-71693000	Strong transcription	Stomach Smooth Muscle	stomach
12	chr16:71681200-71693000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr16:71681200-71693600	Strong transcription	Fetal Intestine Large	intestine
14	chr16:71681200-71710800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr16:71681200-71716000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr16:71681400-71690600	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr16:71681400-71691200	Strong transcription	Fetal Stomach	stomach
18	chr16:71681400-71692800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr16:71681400-71693200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr16:71681400-71693400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr16:71681400-71694200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr16:71681800-71689800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr16:71681800-71690800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr16:71682000-71690800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr16:71682200-71692600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr16:71682800-71698000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr16:71683000-71693000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr16:71683400-71689800	Weak transcription	K562	blood
29	chr16:71683800-71688200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr16:71683800-71688200	Weak transcription	Colonic Mucosa	Colon
31	chr16:71683800-71688400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr16:71683800-71688400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr16:71683800-71689800	Weak transcription	Fetal Thymus	thymus
34	chr16:71683800-71692600	Weak transcription	GM12878-XiMat	blood
35	chr16:71683800-71704800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr16:71683800-71756600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:71684000-71688200	Weak transcription	Thymus	Thymus
38	chr16:71684000-71688200	Weak transcription	NHDF-Ad	bronchial
39	chr16:71684000-71688200	Weak transcription	NHEK	skin
40	chr16:71684000-71688400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr16:71684000-71688400	Weak transcription	Fetal Kidney	kidney
42	chr16:71684000-71688400	Weak transcription	Dnd41	blood
43	chr16:71684000-71692200	Weak transcription	NHLF	lung
44	chr16:71684000-71697800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr16:71684000-71704000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr16:71684200-71688600	Weak transcription	A549	lung
47	chr16:71684400-71691800	Weak transcription	Hela-S3	cervix
48	chr16:71684600-71688200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr16:71684600-71689200	Weak transcription	Colon Smooth Muscle	Colon
50	chr16:71685200-71741200	Weak transcription	Psoas Muscle	Psoas

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