Variant report

Variant	rs4921062
Chromosome Location	chr5:115445812-115445813
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10036669	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10042177	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10043670	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10051072	0.85[ASN][1000 genomes]
rs10051302	0.85[ASN][1000 genomes]
rs10059455	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10065178	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10065554	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10066081	0.85[ASN][1000 genomes]
rs10068479	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075195	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10079176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10079466	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10079691	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10079903	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10463453	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10463676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10478280	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11241352	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241359	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241360	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11241364	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11241365	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11241366	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11241367	0.82[ASN][1000 genomes]
rs11241371	0.83[ASN][1000 genomes]
rs1129494	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1133187	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11738674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11738775	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11739600	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11742938	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11746600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11750725	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11950936	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951865	0.85[ASN][1000 genomes]
rs11952043	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11958648	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054994	0.85[ASN][1000 genomes]
rs12332433	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12656463	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13153586	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13157583	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13162238	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13170042	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13172482	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179593	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13180407	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13181756	0.83[ASN][1000 genomes]
rs13182605	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13184073	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1396478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396479	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396481	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1396482	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1508882	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1588267	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2063249	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2063250	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2063253	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2221676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2416426	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2416427	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2416430	0.84[AFR][1000 genomes]
rs4383750	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4921063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594938	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6594948	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6594951	0.85[ASN][1000 genomes]
rs6594952	0.85[ASN][1000 genomes]
rs6865237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6871968	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6876901	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6879929	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6886944	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6889212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6894046	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6896479	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7703164	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7715759	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7715797	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7728838	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7728852	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7729414	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7730551	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7733128	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7734295	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7735539	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7736189	0.85[ASN][1000 genomes]
rs9326986	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9326987	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1027418	chr5:115206256-115446861	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1030480	chr5:115228889-115446861	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv599479	chr5:115233116-115450969	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv882736	chr5:115254723-115552945	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv882737	chr5:115263853-115552945	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv527320	chr5:115382097-115573543	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1027266	chr5:115382704-115501792	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv1032199	chr5:115384131-115525738	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	esv2830404	chr5:115386661-115490546	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv1019972	chr5:115386860-115563533	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv537869	chr5:115386860-115563533	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv1018861	chr5:115397834-115563533	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	nsv537870	chr5:115397834-115563533	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	esv2762538	chr5:115436508-115455707	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4921062	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115421400-115446400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:115421400-115446400	Weak transcription	Esophagus	oesophagus
3	chr5:115421800-115448000	Weak transcription	Aorta	Aorta
4	chr5:115429400-115448200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:115429400-115448200	Weak transcription	Right Ventricle	heart
6	chr5:115429400-115449000	Weak transcription	Colonic Mucosa	Colon
7	chr5:115429600-115448200	Weak transcription	Small Intestine	intestine
8	chr5:115429600-115448600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:115430200-115448800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:115430600-115447400	Weak transcription	Brain Angular Gyrus	brain
11	chr5:115430800-115446600	Weak transcription	K562	blood
12	chr5:115430800-115447600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:115430800-115448000	Weak transcription	Psoas Muscle	Psoas
14	chr5:115430800-115448600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:115431000-115447000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:115431000-115448200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:115431200-115447600	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:115431200-115447600	Weak transcription	Brain Substantia Nigra	brain
19	chr5:115431200-115448800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr5:115431200-115449800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:115431400-115448400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:115431600-115448200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:115431800-115446000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:115432400-115446000	Weak transcription	A549	lung
25	chr5:115433200-115448600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:115433600-115447400	Weak transcription	GM12878-XiMat	blood
27	chr5:115433600-115448000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:115433600-115457200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:115433800-115447400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr5:115433800-115447400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr5:115433800-115447400	Weak transcription	Dnd41	blood
32	chr5:115434200-115447800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:115434200-115448000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:115434800-115447800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr5:115435000-115448000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:115435000-115448200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:115435200-115448000	Weak transcription	Fetal Lung	lung
38	chr5:115436000-115446200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:115437000-115446000	Weak transcription	Liver	Liver
40	chr5:115437000-115447600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:115437000-115447800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:115437000-115448000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr5:115437000-115448200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:115437200-115446200	Weak transcription	Primary B cells from cord blood	blood
45	chr5:115438200-115448000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:115441000-115451200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:115441600-115446400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:115443800-115446000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:115443800-115450400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
50	chr5:115444000-115448200	Weak transcription	HepG2	liver

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