Variant report

Variant	rs11666213
Chromosome Location	chr19:21605645-21605646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10414834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424079	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666447	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666525	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666540	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11667103	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11667361	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11667392	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11669033	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669790	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11670815	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670868	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11672341	0.88[EUR][1000 genomes]
rs11672583	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11879901	0.88[EUR][1000 genomes]
rs13346641	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1621154	0.87[EUR][1000 genomes]
rs1626404	0.87[EUR][1000 genomes]
rs1762578	0.87[EUR][1000 genomes]
rs17680605	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1781867	0.87[EUR][1000 genomes]
rs1781872	0.87[EUR][1000 genomes]
rs1967182	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2061916	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2154302	0.85[EUR][1000 genomes]
rs2358993	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2359144	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2359145	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562405	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562411	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562413	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562416	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2650776	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650844	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650848	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs279807	0.82[EUR][1000 genomes]
rs279809	0.83[EUR][1000 genomes]
rs2914646	0.84[AFR][1000 genomes]
rs3853837	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321312	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4327181	0.87[EUR][1000 genomes]
rs4359573	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4544364	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4638726	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55756795	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55790393	0.87[EUR][1000 genomes]
rs55875743	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55899865	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs57299552	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58412280	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60173523	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61035285	0.88[EUR][1000 genomes]
rs62107465	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62107469	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62107472	0.87[EUR][1000 genomes]
rs62107479	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107531	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107532	0.88[EUR][1000 genomes]
rs62107534	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107536	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62107539	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62107540	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62107541	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62109225	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62109226	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109227	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs62109228	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs62109229	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62110071	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62110367	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62110377	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62110416	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110420	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110424	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62110426	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110427	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246339	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7251135	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7258099	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7258473	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7258562	0.87[EUR][1000 genomes]
rs73537884	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
15	nsv578953	chr19:21586797-21609607	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11666213	RP11-678G14.2	cis	Whole Blood	GTEx
rs11666213	RP11-678G14.2	cis	Esophagus Muscularis	GTEx
rs11666213	ZNF708	cis	lung	GTEx
rs11666213	ZNF708	cis	Muscle Skeletal	GTEx
rs11666213	ZNF708	cis	Thyroid	GTEx
rs11666213	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs11666213	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21581800-21607000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:21590200-21606400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr19:21590600-21608200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
5	chr19:21591800-21607000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
6	chr19:21593400-21610200	ZNF genes & repeats	Liver	Liver
7	chr19:21593600-21606600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:21598600-21605800	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:21599600-21611000	ZNF genes & repeats	Adipose Nuclei	Adipose
10	chr19:21599800-21606400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr19:21599800-21606400	ZNF genes & repeats	Brain Germinal Matrix	brain
12	chr19:21600000-21613000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:21600200-21606800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:21600200-21608200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:21600800-21606600	ZNF genes & repeats	Primary T cells from cord blood	blood
16	chr19:21600800-21607800	ZNF genes & repeats	Dnd41	blood
17	chr19:21601200-21607600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
18	chr19:21602000-21608200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
19	chr19:21603400-21609400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:21603600-21606200	ZNF genes & repeats	Fetal Kidney	kidney
21	chr19:21604200-21606200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:21604200-21606200	ZNF genes & repeats	Psoas Muscle	Psoas
23	chr19:21604200-21607600	ZNF genes & repeats	Fetal Brain Female	brain
24	chr19:21604400-21606800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:21604400-21609200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
26	chr19:21604400-21610400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
27	chr19:21604600-21605800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:21604600-21605800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
29	chr19:21604600-21606400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:21604600-21606400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
31	chr19:21604600-21606400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr19:21604600-21606400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
33	chr19:21604600-21606400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
34	chr19:21604600-21606600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
35	chr19:21604600-21608000	ZNF genes & repeats	Fetal Lung	lung
36	chr19:21604600-21608400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
37	chr19:21604800-21606400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:21604800-21608800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
39	chr19:21605200-21606000	Weak transcription	HSMM	muscle
40	chr19:21605200-21606400	ZNF genes & repeats	Fetal Heart	heart
41	chr19:21605200-21606600	Weak transcription	Pancreas	Pancrea
42	chr19:21605200-21608000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
43	chr19:21605600-21607200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:21605600-21608000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
45	chr19:21605600-21610800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:21605600-21610800	Weak transcription	Ovary	ovary

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