Variant report

Variant	rs11669790
Chromosome Location	chr19:21511782-21511783
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:21501353..21503397-chr19:21510480..21512126,2	MCF-7	breast:
2	chr19:21510924..21513197-chr19:21688433..21691004,2	MCF-7	breast:
3	chr19:21511427..21512224-chr9:140135317..140136194,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000188229	Chromatin interaction
ENSG00000197013	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10414834	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10424079	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11666213	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11666447	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11666525	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11666540	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11667103	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667361	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11667392	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669033	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11670815	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11670868	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11672341	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11672583	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673320	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11879901	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13346641	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1621154	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626404	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1762578	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680605	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781867	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781872	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967182	0.82[EUR][1000 genomes]
rs2061916	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154302	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2358993	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359144	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2359145	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2562405	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562411	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2562413	0.83[EUR][1000 genomes]
rs2562416	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650776	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650844	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2650848	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs279807	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279809	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853837	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3853838	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4321312	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4327181	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4359573	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544364	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638726	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55756795	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55790393	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55875743	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55899865	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57299552	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58412280	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60173523	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61035285	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62107465	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107468	0.87[EUR][1000 genomes]
rs62107469	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107472	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62107479	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107531	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107532	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62107534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107539	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107540	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107541	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109225	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109226	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62109227	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62109228	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62109229	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62110071	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110367	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62110377	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110416	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62110420	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62110424	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62110426	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62110427	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62110428	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62110429	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7246339	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251135	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258099	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7258473	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258562	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73537884	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv963023	chr19:21491992-21570395	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv3415719	chr19:21511760-21519079	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11669790	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs11669790	RP11-678G14.2	cis	Esophagus Muscularis	GTEx
rs11669790	ZNF708	cis	lung	GTEx
rs11669790	RP11-678G14.2	cis	Whole Blood	GTEx
rs11669790	ZNF708	cis	Muscle Skeletal	GTEx
rs11669790	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21509800-21512600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21510400-21512600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:21510400-21512600	Active TSS	Fetal Brain Female	brain
4	chr19:21510600-21511800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr19:21510600-21512400	Active TSS	Ovary	ovary
6	chr19:21510600-21512400	Active TSS	Hela-S3	cervix
7	chr19:21510800-21511800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr19:21510800-21512200	Active TSS	HMEC	breast
9	chr19:21510800-21512400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr19:21510800-21512400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:21510800-21512400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr19:21510800-21512400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:21510800-21512400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:21510800-21512400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:21510800-21512400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:21510800-21512400	Active TSS	Right Atrium	heart
17	chr19:21510800-21512400	Active TSS	A549	lung
18	chr19:21510800-21512400	Active TSS	GM12878-XiMat	blood
19	chr19:21510800-21512400	Active TSS	NHDF-Ad	bronchial
20	chr19:21510800-21512400	Active TSS	NHLF	lung
21	chr19:21510800-21512600	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr19:21510800-21512600	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr19:21510800-21512600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:21510800-21512600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:21510800-21512600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr19:21510800-21512600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:21510800-21512600	Active TSS	Brain Cingulate Gyrus	brain
28	chr19:21510800-21512600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:21510800-21512600	Active TSS	Fetal Brain Male	brain
30	chr19:21511000-21511800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr19:21511000-21511800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:21511000-21512200	Active TSS	Fetal Muscle Trunk	muscle
33	chr19:21511000-21512400	Active TSS	H9 Cell Line	embryonic stem cell
34	chr19:21511000-21512400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:21511000-21512400	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr19:21511000-21512400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:21511000-21512400	Active TSS	Brain Angular Gyrus	brain
38	chr19:21511000-21512400	Active TSS	Colon Smooth Muscle	Colon
39	chr19:21511000-21512400	Active TSS	Fetal Intestine Large	intestine
40	chr19:21511000-21512600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:21511000-21512600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:21511000-21512600	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr19:21511000-21512600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:21511000-21512600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr19:21511000-21512600	Active TSS	Stomach Smooth Muscle	stomach
46	chr19:21511000-21512600	Active TSS	HSMM	muscle
47	chr19:21511000-21512600	Active TSS	HSMMtube	muscle
48	chr19:21511000-21512600	Active TSS	K562	blood
49	chr19:21511200-21512200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr19:21511200-21512200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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