Variant report

Variant	rs9302469
Chromosome Location	chr16:12462616-12462617
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	CTCF	chr16:12462600-12462750	HepG2	liver:	n/a	chr16:12462644-12462652
2	BHLHE40	chr16:12462564-12462808	K562	blood:	n/a	chr16:12462692-12462701 chr16:12462691-12462700 chr16:12462691-12462700 chr16:12462685-12462706 chr16:12462689-12462702

Variant related genes	Relation type
ENSG00000260723	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11075061	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11645864	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11648255	0.91[EUR][1000 genomes]
rs11648926	0.86[EUR][1000 genomes]
rs12102400	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12102608	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs158467	0.80[EUR][1000 genomes]
rs16959318	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16959342	0.84[EUR][1000 genomes]
rs209846	0.86[EUR][1000 genomes]
rs209851	0.80[EUR][1000 genomes]
rs209853	0.81[EUR][1000 genomes]
rs209856	0.82[EUR][1000 genomes]
rs2856771	0.81[EUR][1000 genomes]
rs289673	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs31679	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs476267	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4780422	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4780423	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4781207	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4781208	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4781209	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4781214	0.81[EUR][1000 genomes]
rs544598	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62039994	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6498278	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6498279	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7184369	0.82[EUR][1000 genomes]
rs7184477	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7190509	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7195981	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7201621	0.89[EUR][1000 genomes]
rs8051758	0.83[EUR][1000 genomes]
rs9284322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9635495	0.83[EUR][1000 genomes]
rs9939036	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12410200-12464800	Weak transcription	Gastric	stomach
2	chr16:12435800-12484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:12443600-12470800	Weak transcription	HepG2	liver
4	chr16:12444800-12491400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr16:12447600-12470000	Weak transcription	Esophagus	oesophagus
6	chr16:12448600-12471200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr16:12449800-12463000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr16:12450800-12470000	Weak transcription	Fetal Thymus	thymus
9	chr16:12452800-12464200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr16:12453000-12470600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr16:12453200-12479000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr16:12453400-12467400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr16:12453400-12469400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr16:12454400-12469200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr16:12454600-12470800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr16:12455600-12479400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr16:12456200-12470600	Weak transcription	NHEK	skin
18	chr16:12456800-12478600	Weak transcription	Ovary	ovary
19	chr16:12457000-12492400	Weak transcription	Lung	lung
20	chr16:12457200-12465000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr16:12457400-12469000	Weak transcription	Brain Angular Gyrus	brain
22	chr16:12457400-12469000	Weak transcription	Brain Anterior Caudate	brain
23	chr16:12457400-12469200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr16:12457400-12497400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr16:12457600-12464400	Weak transcription	Right Atrium	heart
26	chr16:12457600-12464600	Weak transcription	Adipose Nuclei	Adipose
27	chr16:12457600-12491600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr16:12457600-12497400	Weak transcription	Spleen	Spleen
29	chr16:12461000-12463000	Strong transcription	Primary B cells from cord blood	blood
30	chr16:12461000-12464600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr16:12461000-12464600	Weak transcription	Brain Hippocampus Middle	brain
32	chr16:12461000-12464600	Weak transcription	Brain Substantia Nigra	brain
33	chr16:12461000-12471200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr16:12461000-12471600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr16:12461000-12473400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr16:12461200-12470000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr16:12461200-12490200	Weak transcription	GM12878-XiMat	blood
38	chr16:12462000-12470600	Weak transcription	Primary T cells from cord blood	blood
39	chr16:12462200-12462800	Enhancers	Left Ventricle	heart

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