Variant report

Variant	rs9889219
Chromosome Location	chr16:69721415-69721416
allele	A/G
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	chr16:69721294-69721545	HepG2	liver:	n/a	n/a
2	CEBPB	chr16:69721411-69721611	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69718628..69722517-chr16:69722736..69727715,5	MCF-7	breast:

Variant related genes	Relation type
NFAT5	TF binding region
ENSG00000102908	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10517	0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1142105	0.99[ASN][1000 genomes]
rs12921017	0.89[ASN][1000 genomes]
rs13329844	0.86[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs13331055	0.93[ASN][1000 genomes]
rs13331071	0.80[ASN][1000 genomes]
rs13331216	0.96[ASN][1000 genomes]
rs13335149	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13335664	0.96[ASN][1000 genomes]
rs16958997	0.85[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs16959059	0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2304526	0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2917665	0.85[ASN][1000 genomes]
rs2917667	0.81[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2917669	0.81[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2917672	0.82[ASN][1000 genomes]
rs2917673	0.90[ASN][1000 genomes]
rs2917674	0.90[ASN][1000 genomes]
rs2917675	0.86[ASN][1000 genomes]
rs2917676	0.90[ASN][1000 genomes]
rs2917682	0.81[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2917683	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2965752	0.88[ASN][1000 genomes]
rs2965753	0.81[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap]
rs3785075	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3826153	0.85[CHD][hapmap]
rs3826154	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs4247109	0.84[CHD][hapmap]
rs4442796	0.81[CHD][hapmap]
rs4497676	0.80[YRI][hapmap]
rs4985527	0.81[CHD][hapmap]
rs6499246	0.83[ASN][1000 genomes]
rs689452	0.86[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs689456	0.88[ASN][1000 genomes]
rs7200420	0.89[ASN][1000 genomes]
rs7359387	0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9888993	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9921652	0.88[CHD][hapmap]
rs9924264	0.83[ASN][1000 genomes]
rs9924271	0.88[CHD][hapmap]
rs9924953	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9925037	0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs9927809	0.88[ASN][1000 genomes]
rs9934264	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9934321	0.88[ASN][1000 genomes]
rs9934681	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9936464	0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs9937018	0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9938717	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]

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	nsv906822	chr16:69711533-69745145	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9889219	DHODH	cis	cerebellum	SCAN
rs9889219	ATP6V0D1	cis	cerebellum	SCAN
rs9889219	CA7	cis	cerebellum	SCAN
rs9889219	BRF1	trans	parietal	SCAN
rs9889219	HSF4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69667000-69727600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:69671200-69726400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:69681600-69725800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:69681600-69725800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr16:69685000-69724800	Weak transcription	Fetal Heart	heart
6	chr16:69688600-69725400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr16:69690200-69725800	Weak transcription	Ovary	ovary
8	chr16:69691000-69726400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr16:69694800-69725800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr16:69700400-69725400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr16:69701400-69725600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:69701800-69739200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr16:69704000-69725400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr16:69704600-69737800	Strong transcription	Liver	Liver
15	chr16:69705800-69725800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr16:69705800-69725800	Weak transcription	Gastric	stomach
17	chr16:69705800-69725800	Weak transcription	Small Intestine	intestine
18	chr16:69705800-69726000	Weak transcription	Psoas Muscle	Psoas
19	chr16:69706000-69725000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr16:69706000-69726200	Weak transcription	Stomach Mucosa	stomach
21	chr16:69706200-69725800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr16:69706200-69725800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr16:69706200-69725800	Weak transcription	Right Ventricle	heart
24	chr16:69706400-69725800	Weak transcription	Brain Angular Gyrus	brain
25	chr16:69708800-69739600	Strong transcription	Placenta	Placenta
26	chr16:69709000-69739400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:69709400-69721600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:69709600-69723600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr16:69709600-69724600	Strong transcription	Fetal Intestine Large	intestine
31	chr16:69709600-69726800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr16:69709800-69721600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr16:69709800-69737000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr16:69710000-69721600	Strong transcription	Fetal Lung	lung
35	chr16:69710000-69737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr16:69710800-69732000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr16:69711600-69723800	Strong transcription	Fetal Stomach	stomach
38	chr16:69711600-69723800	Weak transcription	K562	blood
39	chr16:69711600-69725600	Weak transcription	Fetal Brain Male	brain
40	chr16:69711800-69723000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr16:69711800-69723800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr16:69711800-69723800	Strong transcription	Fetal Intestine Small	intestine
43	chr16:69712800-69723800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr16:69712800-69725800	Weak transcription	Brain Germinal Matrix	brain
45	chr16:69712800-69725800	Weak transcription	Brain Substantia Nigra	brain
46	chr16:69713000-69724800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr16:69713200-69724400	Weak transcription	Colonic Mucosa	Colon
48	chr16:69713400-69725800	Weak transcription	Esophagus	oesophagus
49	chr16:69713400-69725800	Weak transcription	Thymus	Thymus
50	chr16:69713600-69723800	Weak transcription	Placenta Amnion	Placenta Amnion

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