Variant report

Variant	rs11075901
Chromosome Location	chr16:71790812-71790813
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1058750	1.00[JPT][hapmap]
rs11075904	0.80[ASW][hapmap];0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11075905	0.90[CEU][hapmap]
rs11862723	0.80[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12929547	0.88[EUR][1000 genomes]
rs1392484	0.90[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1423983	0.80[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2032918	0.80[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.84[TSI][hapmap]
rs2052585	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2133773	0.87[EUR][1000 genomes]
rs2247603	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2334877	0.81[ASW][hapmap];0.90[CEU][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4788548	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs4788553	0.82[EUR][1000 genomes]
rs4788557	0.84[EUR][1000 genomes]
rs4788559	0.89[ASW][hapmap];0.90[CEU][hapmap];0.89[LWK][hapmap];0.83[TSI][hapmap]
rs4788810	0.90[CEU][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs4788813	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs4788828	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs6499526	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs6499528	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs6499530	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.84[TSI][hapmap]
rs6499534	0.81[EUR][1000 genomes]
rs6499538	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs6499540	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7186112	0.83[EUR][1000 genomes]
rs7188675	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs7193549	0.80[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7195059	0.81[ASW][hapmap];0.80[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[TSI][hapmap]
rs7202479	1.00[JPT][hapmap]
rs7204118	0.86[EUR][1000 genomes]
rs7204608	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7204967	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7206470	0.80[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7359478	0.87[EUR][1000 genomes]
rs8044144	0.88[AFR][1000 genomes]
rs8052910	0.87[EUR][1000 genomes]
rs8053186	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8055419	0.83[EUR][1000 genomes]
rs889568	0.90[AFR][1000 genomes]
rs9635524	0.81[EUR][1000 genomes]
rs979790	1.00[JPT][hapmap]
rs9929840	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9929985	0.84[EUR][1000 genomes]
rs9930015	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9934301	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9937511	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9939458	0.80[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv1815957	chr16:71790812-71816899	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11075901	MARVELD3	cis	Esophagus Mucosa	GTEx
rs11075901	PHLPP2	cis	Muscle Skeletal	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	chr16:71763600-71793000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr16:71763600-71800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr16:71763600-71801400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr16:71763600-71812400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr16:71763800-71799600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr16:71763800-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr16:71764000-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr16:71764000-71813000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr16:71764800-71802600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr16:71770600-71793000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr16:71770600-71796000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:71770600-71798600	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr16:71770600-71799600	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr16:71770800-71793200	Strong transcription	HSMM	muscle
20	chr16:71770800-71793600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:71770800-71795800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr16:71770800-71799600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr16:71770800-71810600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr16:71770800-71813800	Strong transcription	Liver	Liver
25	chr16:71771000-71793200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr16:71771000-71812200	Strong transcription	Placenta	Placenta
27	chr16:71774400-71792200	Weak transcription	Aorta	Aorta
28	chr16:71777200-71799800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr16:71778400-71791800	Strong transcription	HepG2	liver
30	chr16:71779000-71793000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr16:71779600-71841800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr16:71780000-71821400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr16:71782800-71792200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr16:71783400-71791400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr16:71783800-71820600	Weak transcription	Psoas Muscle	Psoas
36	chr16:71784000-71811200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:71785400-71792800	Strong transcription	Primary B cells from cord blood	blood
38	chr16:71785400-71799800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr16:71785400-71808800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr16:71785600-71793200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr16:71785800-71792800	Strong transcription	HMEC	breast
42	chr16:71786400-71792800	Strong transcription	HUVEC	blood vessel
43	chr16:71786400-71799800	Strong transcription	Adipose Nuclei	Adipose
44	chr16:71786400-71802200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr16:71786400-71805200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr16:71786600-71809800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr16:71786800-71793000	Strong transcription	Brain Germinal Matrix	brain
48	chr16:71786800-71793200	Strong transcription	Dnd41	blood
49	chr16:71786800-71793400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr16:71786800-71793400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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