Variant report

Variant	rs2099540
Chromosome Location	chr16:46656218-46656219
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	FOXA1	chr16:46656194-46656663	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46653721..46656886-chr16:46721851..46724551,4	K562	blood:

Variant related genes	Relation type
SHCBP1	TF binding region
ENSG00000069329	Chromatin interaction
ENSG00000091651	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12934443	1.00[JPT][hapmap]
rs17734120	1.00[JPT][hapmap]
rs33994299	1.00[JPT][hapmap]
rs3743928	1.00[JPT][hapmap]
rs4439788	1.00[ASW][hapmap]
rs712817	1.00[AMR][1000 genomes]
rs7191018	1.00[JPT][hapmap]
rs8053204	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799780	chr16:46386457-46875496	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1848852	chr16:46463746-46659554	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv917899	chr16:46463769-46669332	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1066221	chr16:46463770-46699143	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1060734	chr16:46463770-46768102	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1064289	chr16:46463770-46801977	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS 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	38 gene(s)	inside rSNPs	diseases
7	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
9	esv1806429	chr16:46468179-46659554	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	esv1847767	chr16:46474763-46659354	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	esv1815153	chr16:46474763-46672206	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	esv1797185	chr16:46489836-46731413	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
14	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
15	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
16	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
17	nsv833216	chr16:46501297-46671860	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
18	nsv916976	chr16:46505597-46801868	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
19	nsv526656	chr16:46539392-46846663	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
20	nsv428327	chr16:46556968-46718490	Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46654600-46656600	Enhancers	Fetal Heart	heart
2	chr16:46655400-46656400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr16:46655400-46656800	Flanking Active TSS	HepG2	liver
4	chr16:46655400-46657800	Weak transcription	Pancreas	Pancrea
5	chr16:46655400-46663200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr16:46655600-46656400	Weak transcription	Aorta	Aorta
7	chr16:46655600-46656600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr16:46655600-46656600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr16:46655600-46656600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr16:46655600-46656600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr16:46655600-46656600	Enhancers	Fetal Lung	lung
12	chr16:46655600-46656600	Enhancers	Fetal Stomach	stomach
13	chr16:46655600-46656800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr16:46655600-46656800	Enhancers	Primary hematopoietic stem cells	blood
15	chr16:46655600-46656800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr16:46655600-46656800	Enhancers	Fetal Muscle Leg	muscle
17	chr16:46655600-46658600	Weak transcription	Ovary	ovary
18	chr16:46655600-46661200	Weak transcription	Gastric	stomach
19	chr16:46655600-46661400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr16:46655600-46672600	Weak transcription	Esophagus	oesophagus
21	chr16:46655600-46694200	Weak transcription	Right Ventricle	heart
22	chr16:46655800-46656400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr16:46655800-46656400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr16:46655800-46656400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr16:46655800-46656600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr16:46655800-46656600	Enhancers	Brain Hippocampus Middle	brain
27	chr16:46655800-46656800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr16:46655800-46656800	Enhancers	Osteobl	bone
29	chr16:46655800-46657000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr16:46655800-46663400	Weak transcription	HMEC	breast
31	chr16:46655800-46663600	Weak transcription	HUVEC	blood vessel
32	chr16:46656000-46656600	Enhancers	Duodenum Mucosa	Duodenum
33	chr16:46656000-46663600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr16:46656200-46656400	Enhancers	Dnd41	blood
35	chr16:46656200-46663400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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