Variant report

Variant	rs11862378
Chromosome Location	chr16:12504265-12504266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1019576	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10852347	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10852348	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11075070	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11075071	0.80[EUR][1000 genomes]
rs11641304	0.89[EUR][1000 genomes]
rs11864693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12444071	0.81[EUR][1000 genomes]
rs12922243	0.85[EUR][1000 genomes]
rs12924360	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12926672	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12927878	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12932170	0.83[EUR][1000 genomes]
rs12932341	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1477119	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16959555	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16959556	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1974905	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2098761	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2865239	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851015	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4780427	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4780428	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4780429	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4780431	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4780432	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4780433	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4781220	0.81[ASN][1000 genomes]
rs4781221	0.81[ASN][1000 genomes]
rs4781222	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4781225	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4781226	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4781227	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4781229	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4781232	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4781233	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4781235	0.81[EUR][1000 genomes]
rs6498286	0.86[EUR][1000 genomes]
rs6498288	0.90[EUR][1000 genomes]
rs6498289	0.90[EUR][1000 genomes]
rs6498292	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6498293	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6498294	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6498295	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6498296	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7187130	0.87[EUR][1000 genomes]
rs7187688	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7190294	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7192229	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7192339	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7192549	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7193128	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7198141	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7198154	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7199220	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8043724	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8046923	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8047108	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8047934	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8049186	0.87[EUR][1000 genomes]
rs8052297	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8053319	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8061365	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8062594	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs889809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs889810	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs889811	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9745308	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9746199	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9746397	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9746403	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12476000-12531600	Weak transcription	Right Ventricle	heart
2	chr16:12482400-12510400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:12487400-12506400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr16:12497800-12505000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:12497800-12519600	Weak transcription	Brain Anterior Caudate	brain
6	chr16:12497800-12539800	Weak transcription	Left Ventricle	heart
7	chr16:12498000-12506800	Weak transcription	HSMMtube	muscle
8	chr16:12498000-12510800	Weak transcription	Spleen	Spleen
9	chr16:12498000-12511600	Weak transcription	Fetal Muscle Leg	muscle
10	chr16:12498000-12515400	Weak transcription	Pancreas	Pancrea
11	chr16:12498000-12518600	Weak transcription	Fetal Intestine Small	intestine
12	chr16:12498000-12541200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr16:12498200-12505400	Weak transcription	Gastric	stomach
14	chr16:12498200-12506000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr16:12498200-12510600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr16:12498200-12513200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr16:12498200-12517200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr16:12498400-12505400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr16:12498400-12506000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr16:12498400-12513800	Weak transcription	Aorta	Aorta
21	chr16:12498400-12514200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr16:12498400-12514800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr16:12498400-12516200	Weak transcription	Fetal Stomach	stomach
24	chr16:12498400-12518800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr16:12498400-12523200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr16:12498400-12523600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr16:12498400-12523800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr16:12498400-12564600	Weak transcription	Esophagus	oesophagus
29	chr16:12498600-12507400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr16:12498800-12516600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr16:12498800-12523800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr16:12499200-12511800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr16:12499200-12518200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr16:12499400-12505400	Weak transcription	Adipose Nuclei	Adipose
35	chr16:12499400-12505800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr16:12499400-12512800	Weak transcription	Brain Substantia Nigra	brain
37	chr16:12499400-12517200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr16:12499400-12527000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr16:12499600-12512800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr16:12501000-12510400	Weak transcription	Lung	lung
41	chr16:12501400-12507200	Weak transcription	GM12878-XiMat	blood
42	chr16:12501600-12504800	Weak transcription	Primary B cells from cord blood	blood
43	chr16:12501600-12504800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr16:12501600-12505800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr16:12501800-12505400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr16:12501800-12510000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr16:12501800-12514000	Weak transcription	NHEK	skin
48	chr16:12501800-12514200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:12501800-12515600	Weak transcription	NHDF-Ad	bronchial
50	chr16:12501800-12519600	Weak transcription	Brain Hippocampus Middle	brain

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