Variant report

Variant	rs4780423
Chromosome Location	chr16:12456485-12456486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11075061	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11075062	0.83[EUR][1000 genomes]
rs11645864	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11648255	0.95[EUR][1000 genomes]
rs11648926	0.83[EUR][1000 genomes]
rs12102400	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12102608	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12445569	0.81[EUR][1000 genomes]
rs16959318	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs176717	0.81[EUR][1000 genomes]
rs209846	0.89[EUR][1000 genomes]
rs209849	0.82[EUR][1000 genomes]
rs209850	0.82[EUR][1000 genomes]
rs209851	0.83[EUR][1000 genomes]
rs209853	0.84[EUR][1000 genomes]
rs209855	0.82[EUR][1000 genomes]
rs209856	0.85[EUR][1000 genomes]
rs289673	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs31679	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs476267	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4780422	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4781201	0.81[EUR][1000 genomes]
rs4781207	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4781208	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4781209	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4781211	0.83[EUR][1000 genomes]
rs4781214	0.83[EUR][1000 genomes]
rs544598	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62039994	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6498277	0.84[EUR][1000 genomes]
rs6498278	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6498279	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7184477	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7190509	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7195981	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7199556	0.80[EUR][1000 genomes]
rs7201621	0.93[EUR][1000 genomes]
rs7202201	0.84[EUR][1000 genomes]
rs7203117	0.83[EUR][1000 genomes]
rs9284322	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9302469	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9939036	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[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	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	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
2	chr16:12410000-12456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:12410200-12464800	Weak transcription	Gastric	stomach
4	chr16:12428400-12461200	Weak transcription	Thymus	Thymus
5	chr16:12434600-12460200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:12435800-12484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr16:12436200-12456800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:12437400-12456600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr16:12443200-12456600	Weak transcription	Spleen	Spleen
10	chr16:12443200-12456800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr16:12443200-12456800	Weak transcription	Psoas Muscle	Psoas
12	chr16:12443200-12456800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr16:12443200-12457000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr16:12443600-12470800	Weak transcription	HepG2	liver
15	chr16:12444800-12491400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr16:12447600-12470000	Weak transcription	Esophagus	oesophagus
17	chr16:12448400-12456600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr16:12448600-12460400	Weak transcription	Fetal Stomach	stomach
19	chr16:12448600-12471200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr16:12448800-12456600	Weak transcription	HSMMtube	muscle
21	chr16:12449000-12456600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr16:12449000-12457400	Weak transcription	Colon Smooth Muscle	Colon
23	chr16:12449400-12456600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr16:12449800-12463000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr16:12450800-12470000	Weak transcription	Fetal Thymus	thymus
26	chr16:12452800-12464200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr16:12453000-12461000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr16:12453000-12470600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr16:12453200-12479000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr16:12453400-12456600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr16:12453400-12467400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr16:12453400-12469400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr16:12454400-12460000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr16:12454400-12469200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr16:12454600-12456600	Weak transcription	Fetal Muscle Leg	muscle
36	chr16:12454600-12460800	Weak transcription	GM12878-XiMat	blood
37	chr16:12454600-12470800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr16:12454800-12458000	Weak transcription	Primary T cells from cord blood	blood
39	chr16:12454800-12458800	Strong transcription	Primary B cells from cord blood	blood
40	chr16:12455000-12458600	Weak transcription	Pancreas	Pancrea
41	chr16:12455600-12479400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr16:12455800-12457400	Enhancers	Brain Cingulate Gyrus	brain
43	chr16:12455800-12457400	Enhancers	Brain Substantia Nigra	brain
44	chr16:12456000-12457200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr16:12456000-12457400	Enhancers	Brain Anterior Caudate	brain
46	chr16:12456000-12457400	Enhancers	Fetal Heart	heart
47	chr16:12456000-12457600	Enhancers	Brain Hippocampus Middle	brain
48	chr16:12456000-12457600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr16:12456200-12456600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr16:12456200-12457000	Enhancers	Lung	lung

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