Variant report

Variant	rs350254
Chromosome Location	chr16:12203789-12203790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1641850	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1641855	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs168414	0.90[EUR][1000 genomes]
rs1704112	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1704116	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs183008	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183010	0.94[EUR][1000 genomes]
rs193252	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2664186	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350203	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350207	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350209	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350210	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs350226	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350231	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs350232	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs350245	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350248	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350251	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350252	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350255	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350256	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350271	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs350272	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350274	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350275	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350277	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350278	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350279	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350285	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350287	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4781187	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9922788	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	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
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1039492	chr16:12176517-12210702	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs350254	SNX29	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12184400-12231200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:12186800-12213400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:12189600-12204000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr16:12189600-12204800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr16:12189600-12204800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr16:12189800-12205000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr16:12189800-12209600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr16:12189800-12220400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr16:12190000-12220200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr16:12190000-12220400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr16:12190200-12210600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr16:12190800-12210600	Weak transcription	Pancreas	Pancrea
13	chr16:12191200-12223200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr16:12191400-12213600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr16:12191800-12205000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr16:12191800-12207800	Weak transcription	Osteobl	bone
17	chr16:12192000-12206000	Weak transcription	Brain Substantia Nigra	brain
18	chr16:12192000-12213800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr16:12192000-12214600	Weak transcription	Right Atrium	heart
20	chr16:12192200-12207200	Weak transcription	HSMMtube	muscle
21	chr16:12192400-12204000	Weak transcription	Liver	Liver
22	chr16:12192400-12206400	Weak transcription	Brain Hippocampus Middle	brain
23	chr16:12192400-12210400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr16:12192400-12213200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr16:12192400-12213200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr16:12192600-12205000	Weak transcription	Brain Anterior Caudate	brain
27	chr16:12192800-12205200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr16:12192800-12205400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr16:12192800-12207000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr16:12192800-12213600	Weak transcription	Adipose Nuclei	Adipose
31	chr16:12193000-12207000	Weak transcription	Fetal Thymus	thymus
32	chr16:12193000-12207600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr16:12193800-12207000	Weak transcription	Esophagus	oesophagus
34	chr16:12193800-12207400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr16:12194000-12212600	Weak transcription	Ovary	ovary
36	chr16:12194000-12213000	Weak transcription	Right Ventricle	heart
37	chr16:12194000-12215200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr16:12194200-12210600	Weak transcription	NHEK	skin
39	chr16:12195800-12203800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr16:12198200-12227800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr16:12198600-12206200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr16:12200200-12205000	Weak transcription	Fetal Stomach	stomach
43	chr16:12200200-12220200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr16:12200400-12206000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr16:12200400-12207400	Weak transcription	Spleen	Spleen
46	chr16:12200400-12209200	Weak transcription	Gastric	stomach
47	chr16:12200400-12210600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr16:12200400-12210600	Weak transcription	Aorta	Aorta
49	chr16:12200600-12206600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr16:12200600-12210400	Weak transcription	Lung	lung

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