Variant report

Variant	rs169773
Chromosome Location	chr16:12625171-12625172
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11075087	0.87[ASN][1000 genomes]
rs12927840	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1543784	0.82[ASN][1000 genomes]
rs1794304	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs210720	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs210721	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs210722	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs210724	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269445	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2269446	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2269447	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269448	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3213481	0.88[ASN][1000 genomes]
rs6498318	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7196897	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1038535	chr16:12620736-12636982	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs169773	TNFRSF17	cis	parietal	SCAN
rs169773	ATF7IP2	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12601400-12625400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr16:12603200-12626400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr16:12605800-12632200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr16:12606000-12632000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr16:12606200-12632400	Weak transcription	Right Atrium	heart
6	chr16:12607000-12625600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr16:12607800-12626200	Weak transcription	Brain Germinal Matrix	brain
8	chr16:12608000-12632400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr16:12610000-12632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr16:12610800-12632200	Weak transcription	Psoas Muscle	Psoas
11	chr16:12611600-12632400	Weak transcription	Left Ventricle	heart
12	chr16:12612000-12625400	Weak transcription	Ovary	ovary
13	chr16:12612400-12626600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr16:12612400-12626600	Weak transcription	Right Ventricle	heart
15	chr16:12612400-12632000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:12612600-12626400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr16:12613000-12625400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr16:12613000-12670800	Weak transcription	Pancreas	Pancrea
19	chr16:12616000-12626600	Weak transcription	Thymus	Thymus
20	chr16:12617000-12626600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr16:12617400-12627000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr16:12618600-12626200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr16:12619000-12626000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr16:12619000-12632200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr16:12619800-12632000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr16:12620600-12625400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr16:12620600-12630200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr16:12620800-12625400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr16:12620800-12625400	Weak transcription	Liver	Liver
30	chr16:12621000-12632400	Weak transcription	Adipose Nuclei	Adipose
31	chr16:12621600-12625800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr16:12621600-12628000	Weak transcription	GM12878-XiMat	blood
33	chr16:12622400-12625800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr16:12623000-12625400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr16:12623000-12625600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr16:12623600-12625600	Enhancers	Duodenum Mucosa	Duodenum
37	chr16:12623600-12627200	Enhancers	Brain Hippocampus Middle	brain
38	chr16:12623800-12625400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr16:12623800-12627000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr16:12623800-12627400	Enhancers	Brain Substantia Nigra	brain
41	chr16:12624000-12625200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr16:12624000-12625400	Weak transcription	Placenta	Placenta
43	chr16:12624000-12625400	Weak transcription	Gastric	stomach
44	chr16:12624000-12625600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr16:12624000-12631600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr16:12624000-12632000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr16:12624000-12632400	Weak transcription	Aorta	Aorta
48	chr16:12624000-12632600	Weak transcription	Lung	lung
49	chr16:12624200-12625200	Weak transcription	Esophagus	oesophagus
50	chr16:12624200-12625400	Weak transcription	Brain Angular Gyrus	brain

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