Variant report

Variant	rs9930778
Chromosome Location	chr16:12492890-12492891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12923656	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6498291	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7201310	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7205270	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9929233	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	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
6	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
7	nsv1736	chr16:12477807-12522707	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1046002	chr16:12482003-12510643	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9930778	NDE1	cis	parietal	SCAN
rs9930778	C16orf63	cis	parietal	SCAN
rs9930778	PARN	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12457400-12497400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr16:12457600-12497400	Weak transcription	Spleen	Spleen
3	chr16:12470200-12497400	Weak transcription	Left Ventricle	heart
4	chr16:12471200-12494200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr16:12471800-12493400	Weak transcription	Aorta	Aorta
6	chr16:12471800-12495800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr16:12471800-12499000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr16:12473800-12493800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr16:12476000-12531600	Weak transcription	Right Ventricle	heart
10	chr16:12478600-12497400	Weak transcription	Pancreas	Pancrea
11	chr16:12480200-12493600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr16:12480800-12497400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr16:12481800-12496800	Weak transcription	Esophagus	oesophagus
14	chr16:12482400-12510400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr16:12484600-12493200	Weak transcription	Fetal Stomach	stomach
16	chr16:12484600-12497200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr16:12485000-12493600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr16:12485000-12493600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr16:12485000-12497000	Weak transcription	NHLF	lung
20	chr16:12485000-12497400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr16:12485000-12501000	Weak transcription	NHEK	skin
22	chr16:12485400-12494400	Strong transcription	Primary B cells from cord blood	blood
23	chr16:12486400-12497400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr16:12486600-12493800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr16:12487000-12496400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr16:12487000-12497400	Weak transcription	Brain Anterior Caudate	brain
27	chr16:12487000-12497400	Weak transcription	Thymus	Thymus
28	chr16:12487000-12497800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr16:12487200-12493000	Weak transcription	Brain Hippocampus Middle	brain
30	chr16:12487200-12497400	Weak transcription	Colon Smooth Muscle	Colon
31	chr16:12487400-12497200	Weak transcription	Gastric	stomach
32	chr16:12487400-12497400	Weak transcription	Brain Substantia Nigra	brain
33	chr16:12487400-12506400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr16:12487600-12493200	Weak transcription	Adipose Nuclei	Adipose
35	chr16:12487600-12497400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr16:12487600-12497400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr16:12487600-12497400	Weak transcription	HSMMtube	muscle
38	chr16:12487800-12497200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr16:12487800-12499600	Weak transcription	Psoas Muscle	Psoas
40	chr16:12488000-12496800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr16:12488000-12497400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr16:12488200-12499200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr16:12489600-12501000	Weak transcription	NHDF-Ad	bronchial
44	chr16:12489800-12497400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr16:12490200-12499400	Strong transcription	Primary T cells from cord blood	blood
46	chr16:12490400-12497400	Weak transcription	Liver	Liver
47	chr16:12490800-12493200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr16:12491600-12493000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr16:12491600-12494200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr16:12491800-12494600	Strong transcription	Monocytes-CD14+_RO01746	blood

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