Variant report

Variant	rs72800847
Chromosome Location	chr16:31022639-31022640
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	ZNF263	chr16:31022546-31023038	HEK293-T-REx	kidney:	n/a	chr16:31022728-31022737
2	REST	chr16:31021051-31022768	H1-neurons	neurons:	n/a	chr16:31021227-31021237 chr16:31022728-31022741 chr16:31021502-31021511

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:31010991..31014838-chr16:31020635..31023865,5	MCF-7	breast:
2	chr16:31021441..31023477-chr16:31083604..31085649,2	MCF-7	breast:

Variant related genes	Relation type
STX1B	TF binding region
ENSG00000099365	Chromatin interaction
ENSG00000167394	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1108431	0.80[EUR][1000 genomes]
rs11150601	0.81[EUR][1000 genomes]
rs12445568	0.89[EUR][1000 genomes]
rs12447930	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12920772	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13708	0.82[EUR][1000 genomes]
rs1870293	0.81[EUR][1000 genomes]
rs2199036	0.88[EUR][1000 genomes]
rs2305880	0.82[EUR][1000 genomes]
rs28360557	0.81[EUR][1000 genomes]
rs34454770	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4889525	0.81[EUR][1000 genomes]
rs55979739	0.82[EUR][1000 genomes]
rs61239537	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6950	0.81[EUR][1000 genomes]
rs7184567	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7203999	0.92[EUR][1000 genomes]
rs729482	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732172	0.81[EUR][1000 genomes]
rs732173	0.82[EUR][1000 genomes]
rs7500176	0.80[EUR][1000 genomes]
rs8060857	0.84[EUR][1000 genomes]
rs8062719	0.85[EUR][1000 genomes]
rs897986	0.81[EUR][1000 genomes]
rs9938550	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
5	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
6	nsv833191	chr16:30864242-31048051	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	115 gene(s)	inside rSNPs	diseases
7	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
8	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
9	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
10	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
11	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
12	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
13	nsv916994	chr16:30971725-31078117	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
14	esv3410149	chr16:31020876-31023424	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
15	esv3407754	chr16:31020976-31023274	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs72800847	RP11-196G11.2	cis	lung	GTEx
rs72800847	HSD3B7	cis	Muscle Skeletal	GTEx
rs72800847	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs72800847	STX4	cis	Nerve Tibial	GTEx
rs72800847	STX1B	cis	Thyroid	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31009200-31034400	Weak transcription	Right Atrium	heart
2	chr16:31018000-31027400	Weak transcription	A549	lung
3	chr16:31020400-31023000	Active TSS	Brain Cingulate Gyrus	brain
4	chr16:31021400-31022800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:31021400-31022800	Active TSS	Fetal Brain Female	brain
6	chr16:31021600-31022800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr16:31022000-31023000	Enhancers	Fetal Brain Male	brain
8	chr16:31022200-31022800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:31022200-31022800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr16:31022200-31022800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr16:31022200-31023000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr16:31022200-31023000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr16:31022400-31022800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr16:31022400-31022800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
15	chr16:31022400-31022800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr16:31022400-31022800	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
17	chr16:31022400-31022800	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr16:31022400-31022800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
19	chr16:31022400-31022800	Bivalent Enhancer	Right Ventricle	heart
20	chr16:31022400-31023200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
21	chr16:31022600-31022800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:31022600-31022800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr16:31022600-31022800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr16:31022600-31022800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr16:31022600-31022800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr16:31022600-31022800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:31022600-31022800	Bivalent Enhancer	Primary T cells from cord blood	blood
28	chr16:31022600-31022800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr16:31022600-31022800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
30	chr16:31022600-31022800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
31	chr16:31022600-31022800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr16:31022600-31022800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
33	chr16:31022600-31022800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
34	chr16:31022600-31022800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr16:31022600-31022800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr16:31022600-31022800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
37	chr16:31022600-31022800	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr16:31022600-31022800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
39	chr16:31022600-31022800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr16:31022600-31022800	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr16:31022600-31022800	Bivalent Enhancer	Fetal Stomach	stomach
42	chr16:31022600-31022800	Bivalent Enhancer	Fetal Thymus	thymus
43	chr16:31022600-31022800	Enhancers	NH-A	brain
44	chr16:31022600-31022800	Bivalent Enhancer	Osteobl	bone
45	chr16:31022600-31023000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr16:31022600-31027200	Weak transcription	Pancreas	Pancrea

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