Variant report

Variant	rs12716979
Chromosome Location	chr16:31011821-31011822
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31004363..31015645-chr16:31042809..31047717,18	MCF-7	breast:
2	chr16:31011772..31015018-chr16:31043547..31045573,3	MCF-7	breast:
3	chr16:31007054..31011428-chr16:31011544..31016044,11	MCF-7	breast:
4	chr16:31010991..31014838-chr16:31020635..31023865,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099365	Chromatin interaction
ENSG00000103496	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4889606	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9926533	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv905737	chr16:30900235-31014179	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription 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	95 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12716979	RP11-196G11.2	cis	Muscle Skeletal	GTEx
rs12716979	HSD3B7	cis	Whole Blood	GTEx
rs12716979	KAT8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30997600-31013600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:31009000-31013200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr16:31009000-31013800	Enhancers	Liver	Liver
4	chr16:31009000-31020400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr16:31009200-31012200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr16:31009200-31013200	Weak transcription	Fetal Heart	heart
7	chr16:31009200-31013200	Weak transcription	Left Ventricle	heart
8	chr16:31009200-31013200	Weak transcription	Right Ventricle	heart
9	chr16:31009200-31013600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr16:31009200-31013600	Weak transcription	Brain Anterior Caudate	brain
11	chr16:31009200-31013600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr16:31009200-31013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr16:31009200-31020400	Weak transcription	Brain Angular Gyrus	brain
14	chr16:31009200-31034400	Weak transcription	Right Atrium	heart
15	chr16:31009400-31012000	Enhancers	Adipose Nuclei	Adipose
16	chr16:31009400-31015000	Enhancers	Placenta	Placenta
17	chr16:31009400-31020600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr16:31009600-31013000	Enhancers	NHEK	skin
19	chr16:31009600-31013200	Weak transcription	Pancreas	Pancrea
20	chr16:31009800-31012200	Weak transcription	Esophagus	oesophagus
21	chr16:31009800-31013200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr16:31009800-31013400	Weak transcription	Fetal Stomach	stomach
23	chr16:31009800-31013800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr16:31009800-31014200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr16:31009800-31021000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr16:31010000-31013200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr16:31010200-31013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr16:31010200-31020800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr16:31010600-31012800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr16:31010600-31012800	Weak transcription	HMEC	breast
31	chr16:31010600-31017600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr16:31010800-31013000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr16:31010800-31013000	Weak transcription	K562	blood
34	chr16:31011000-31012000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr16:31011000-31012800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr16:31011000-31013200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr16:31011000-31013600	Weak transcription	HSMMtube	muscle
38	chr16:31011000-31017000	Weak transcription	Fetal Brain Female	brain
39	chr16:31011200-31012000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr16:31011200-31012200	Weak transcription	Hela-S3	cervix
41	chr16:31011200-31012600	Strong transcription	Brain Germinal Matrix	brain
42	chr16:31011200-31012800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr16:31011200-31013000	Weak transcription	Fetal Intestine Small	intestine
44	chr16:31011200-31013000	Enhancers	HepG2	liver
45	chr16:31011200-31013200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr16:31011200-31013200	Weak transcription	Ovary	ovary
47	chr16:31011200-31013200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr16:31011200-31013400	Weak transcription	Fetal Muscle Leg	muscle
49	chr16:31011200-31014000	Weak transcription	NH-A	brain
50	chr16:31011200-31016800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links