Variant report

Variant	rs9302628
Chromosome Location	chr16:71700504-71700505
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr16:71700258-71700755	HepG2	liver:	n/a	n/a
2	FOXA1	chr16:71700211-71701621	HepG2	liver:	n/a	n/a
3	NFIC	chr16:71700206-71701251	HepG2	liver:	n/a	n/a
4	HNF4A	chr16:71700201-71700527	HepG2	liver:	n/a	n/a
5	ARID3A	chr16:71700485-71701541	HepG2	liver:	n/a	n/a
6	CEBPB	chr16:71700221-71700515	HepG2	liver:	n/a	chr16:71700366-71700377
7	FOXA2	chr16:71700411-71701558	HepG2	liver:	n/a	n/a
8	FOXA1	chr16:71700240-71701293	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71659983..71661516-chr16:71697596..71700523,2	MCF-7	breast:

Variant related genes	Relation type
PHLPP2	TF binding region
ENSG00000140832	Chromatin interaction
ENSG00000260593	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11075896	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11075897	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13331092	1.00[ASW][hapmap];0.88[LWK][hapmap]
rs13331951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13333988	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334187	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334255	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334566	0.91[AFR][1000 genomes]
rs13337162	0.96[AFR][1000 genomes]
rs13337224	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338868	0.88[LWK][hapmap]
rs13339574	0.92[AFR][1000 genomes]
rs28436203	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28487278	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28556848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28649987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28681277	0.93[AFR][1000 genomes]
rs28712876	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28744680	0.83[AFR][1000 genomes]
rs28757746	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34113755	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55829421	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55930830	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56209933	0.83[AFR][1000 genomes]
rs57187537	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57827931	0.92[AFR][1000 genomes]
rs58324033	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60173154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61258964	0.82[AFR][1000 genomes]
rs6499544	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs7191105	0.82[YRI][hapmap]
rs7196013	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7198645	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73578257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73580232	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582208	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582231	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8045394	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs8048170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8059131	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8062948	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8063658	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9302626	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs9921383	1.00[ASW][hapmap];0.94[MKK][hapmap]
rs9921552	0.96[AFR][1000 genomes]
rs9923154	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9924829	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9924862	0.96[AFR][1000 genomes]
rs9925371	0.93[AFR][1000 genomes]
rs9925712	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926077	0.93[AFR][1000 genomes]
rs9927004	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928298	1.00[ASW][hapmap];0.94[LWK][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930271	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930588	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933587	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9934778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9935867	0.96[AFR][1000 genomes];1.00[AMR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9302628	MARVELD3	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 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	chr16:71681200-71710800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr16:71681200-71716000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr16:71683800-71704800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:71683800-71756600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:71684000-71704000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr16:71685200-71741200	Weak transcription	Psoas Muscle	Psoas
12	chr16:71685400-71718800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr16:71685800-71726000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr16:71686200-71705400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr16:71686800-71703000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr16:71686800-71717200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr16:71687800-71725000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr16:71688600-71703400	Weak transcription	Pancreas	Pancrea
19	chr16:71688600-71704000	Weak transcription	Gastric	stomach
20	chr16:71689000-71703200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr16:71689000-71710000	Weak transcription	Thymus	Thymus
22	chr16:71690600-71701000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr16:71690600-71702800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr16:71690600-71703200	Weak transcription	Lung	lung
25	chr16:71690600-71703400	Weak transcription	Right Ventricle	heart
26	chr16:71690600-71706400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr16:71690600-71708800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr16:71690600-71709600	Weak transcription	Small Intestine	intestine
29	chr16:71690600-71733600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr16:71690600-71741200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr16:71690800-71725600	Weak transcription	Fetal Thymus	thymus
32	chr16:71691200-71703800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr16:71692800-71701200	Weak transcription	Hela-S3	cervix
34	chr16:71692800-71703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr16:71693000-71700600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr16:71693000-71701000	Weak transcription	Brain Angular Gyrus	brain
37	chr16:71693000-71702800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr16:71693000-71703000	Weak transcription	NHLF	lung
39	chr16:71693000-71704000	Weak transcription	Fetal Heart	heart
40	chr16:71693000-71756400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr16:71694400-71705600	Strong transcription	Fetal Stomach	stomach
42	chr16:71694600-71706600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr16:71694800-71710400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr16:71695000-71707400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr16:71695000-71710800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr16:71695000-71725200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr16:71695000-71726000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr16:71695200-71719200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr16:71695200-71724800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr16:71695200-71725200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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