Variant report

Variant	rs6565280
Chromosome Location	chr16:31767520-31767521
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10871458	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11150638	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1156903	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11644104	0.89[CEU][hapmap]
rs12324951	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12447780	0.85[ASN][1000 genomes]
rs12716999	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12717000	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1406177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1528319	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1534507	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1852666	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1881316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1919040	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1919042	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2078924	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2106579	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2106581	0.98[ASN][1000 genomes]
rs2157970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2178179	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2188619	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2222754	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2359219	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2359222	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2359226	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359455	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28427454	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2884713	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4620975	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4889553	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889555	0.94[CEU][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889688	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889689	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4889693	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62054710	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6565267	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6565269	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6565275	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6565278	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6565282	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6565285	0.93[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6565286	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6565287	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67922432	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7188627	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190730	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7191481	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7206536	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs727349	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8048591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8049323	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8053712	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8060086	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062424	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8062902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs916753	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921546	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9921898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9928006	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9929892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9930700	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9936002	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
2	esv3344221	chr16:31526786-31821640	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	esv3323903	chr16:31526802-31821640	Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv3504445	chr16:31526873-31821580	Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	esv3504446	chr16:31526873-31821580	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	esv3366795	chr16:31534951-31827424	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1067321	chr16:31652036-31959992	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
8	nsv918074	chr16:31669781-31935033	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv1063037	chr16:31669981-31934894	Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv542903	chr16:31669981-31934894	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv905761	chr16:31730525-31812442	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv3446880	chr16:31734687-31891223	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6565280	CLUHP3	cis	Whole Blood	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31755400-31771000	ZNF genes & repeats	Liver	Liver
2	chr16:31756400-31771000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:31759600-31769200	ZNF genes & repeats	Colon Smooth Muscle	Colon
4	chr16:31759600-31769400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
5	chr16:31759600-31769600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
6	chr16:31759600-31769600	ZNF genes & repeats	HepG2	liver
7	chr16:31759600-31769800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
8	chr16:31759600-31770000	ZNF genes & repeats	Primary B cells from cord blood	blood
9	chr16:31759600-31770000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
10	chr16:31759600-31770200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr16:31759600-31770800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr16:31759600-31771000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr16:31759600-31771000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
14	chr16:31759600-31771000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:31759600-31771000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr16:31759600-31771000	ZNF genes & repeats	Adipose Nuclei	Adipose
17	chr16:31759600-31771000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr16:31759800-31769200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
19	chr16:31759800-31769400	ZNF genes & repeats	Primary T cells from cord blood	blood
20	chr16:31759800-31769400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
21	chr16:31759800-31769600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr16:31759800-31769600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
23	chr16:31759800-31769600	ZNF genes & repeats	Brain Hippocampus Middle	brain
24	chr16:31759800-31770000	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
25	chr16:31759800-31770000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
26	chr16:31759800-31770800	ZNF genes & repeats	Brain Anterior Caudate	brain
27	chr16:31759800-31771000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
28	chr16:31759800-31771000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr16:31759800-31772600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
30	chr16:31759800-31788600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr16:31760000-31769600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr16:31760000-31769600	ZNF genes & repeats	Brain Substantia Nigra	brain
33	chr16:31760200-31771000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
34	chr16:31761200-31768400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr16:31761200-31768600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr16:31762400-31768400	Weak transcription	Lung	lung
37	chr16:31762800-31771000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr16:31763200-31769800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
39	chr16:31763200-31770000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
40	chr16:31763200-31770200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr16:31763200-31771000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr16:31763400-31769000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr16:31763400-31770000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr16:31763400-31771000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
45	chr16:31763600-31768800	ZNF genes & repeats	GM12878-XiMat	blood
46	chr16:31763600-31769200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
47	chr16:31763600-31769400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
48	chr16:31763600-31769600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr16:31763600-31770000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
50	chr16:31763600-31770800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum

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