Variant report

Variant	rs11668682
Chromosome Location	chr19:21666161-21666162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr19:21665533-21666181	H1-hESC	embryonic stem cell:	n/a	chr19:21666133-21666143 chr19:21665751-21665770
2	BRCA1	chr19:21665696-21666181	HepG2	liver:	n/a	n/a
3	JUND	chr19:21665695-21666179	K562	blood:	n/a	chr19:21665987-21665998
4	TBP	chr19:21665803-21666181	Hela-S3	cervix:	n/a	n/a
5	MAZ	chr19:21665695-21666181	GM12878	blood:	n/a	n/a
6	MXI1	chr19:21665805-21666179	K562	blood:	n/a	n/a
7	EP300	chr19:21665803-21666181	GM12878	blood:	n/a	chr19:21665901-21665917 chr19:21666082-21666098 chr19:21666091-21666107
8	TBP	chr19:21665694-21666182	K562	blood:	n/a	n/a
9	ZNF143	chr19:21665629-21666181	K562	blood:	n/a	n/a
10	ELK1	chr19:21665666-21666180	K562	blood:	n/a	n/a
11	TBP	chr19:21665695-21666182	HepG2	liver:	n/a	n/a
12	BRCA1	chr19:21665696-21666178	Hela-S3	cervix:	n/a	n/a
13	CUX1	chr19:21665804-21666180	K562	blood:	n/a	n/a
14	SMC3	chr19:21665623-21666178	Hela-S3	cervix:	n/a	chr19:21665755-21665769
15	EBF1	chr19:21665697-21666178	GM12878	blood:	n/a	n/a
16	CHD2	chr19:21665694-21666178	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr19:21665543-21666179	HepG2	liver:	n/a	chr19:21666133-21666143 chr19:21665751-21665770
18	CHD1	chr19:21665792-21666181	GM12878	blood:	n/a	n/a
19	CHD2	chr19:21665695-21666181	HepG2	liver:	n/a	n/a
20	HCFC1	chr19:21665694-21666180	K562	blood:	n/a	n/a
21	GTF2F1	chr19:21665694-21666181	H1-hESC	embryonic stem cell:	n/a	n/a
22	HMGN3	chr19:21665694-21666181	K562	blood:	n/a	n/a
23	ZKSCAN1	chr19:21665805-21666177	Hela-S3	cervix:	n/a	n/a
24	RCOR1	chr19:21665792-21666182	GM12878	blood:	n/a	n/a
25	USF2	chr19:21665804-21666180	GM12878	blood:	n/a	chr19:21665881-21665897
26	CTCF	chr19:21665592-21666181	GM12878	blood:	n/a	chr19:21665789-21665802 chr19:21665753-21665771 chr19:21665755-21665768 chr19:21665874-21665887 chr19:21665754-21665770 chr19:21665755-21665768
27	CHD2	chr19:21665694-21666181	K562	blood:	n/a	n/a
28	FOS	chr19:21665968-21666168	MCF10A-Er-Src	breast:	n/a	n/a
29	STAT1	chr19:21665696-21666181	GM12878	blood:	n/a	chr19:21665722-21665730
30	TBL1XR1	chr19:21665695-21666179	GM12878	blood:	n/a	n/a
31	CTCF	chr19:21665618-21666175	IMR90	lung:	n/a	chr19:21665789-21665802 chr19:21665753-21665771 chr19:21665755-21665768 chr19:21665874-21665887 chr19:21665754-21665770 chr19:21665755-21665768
32	ZNF143	chr19:21665697-21666180	Hela-S3	cervix:	n/a	n/a
33	CEBPB	chr19:21665804-21666165	Hela-S3	cervix:	n/a	n/a
34	RFX5	chr19:21665697-21666181	HepG2	liver:	n/a	n/a
35	CTCF	chr19:21665566-21666181	K562	blood:	n/a	chr19:21665789-21665802 chr19:21665753-21665771 chr19:21665755-21665768 chr19:21665874-21665887 chr19:21665754-21665770 chr19:21665755-21665768
36	RCOR1	chr19:21665696-21666180	K562	blood:	n/a	n/a
37	BHLHE40	chr19:21665697-21666181	GM12878	blood:	n/a	chr19:21665881-21665897
38	BACH1	chr19:21665696-21666180	K562	blood:	n/a	n/a
39	TAL1	chr19:21665697-21666180	K562	blood:	n/a	n/a
40	MAFK	chr19:21665804-21666165	Hela-S3	cervix:	n/a	n/a
41	ZNF263	chr19:21665697-21666246	K562	blood:	n/a	n/a
42	RFX5	chr19:21665792-21666179	GM12878	blood:	n/a	n/a
43	SMC3	chr19:21665584-21666180	K562	blood:	n/a	chr19:21665755-21665769
44	GTF2F1	chr19:21665806-21666180	Hela-S3	cervix:	n/a	n/a
45	UBTF	chr19:21665803-21666177	K562	blood:	n/a	n/a
46	ZNF384	chr19:21665583-21666175	K562	blood:	n/a	n/a
47	USF2	chr19:21665807-21666179	K562	blood:	n/a	chr19:21665881-21665897
48	TBP	chr19:21665792-21666181	GM12878	blood:	n/a	n/a
49	TBL1XR1	chr19:21665694-21666181	K562	blood:	n/a	n/a
50	MAFK	chr19:21665803-21666180	K562	blood:	n/a	n/a

Variant related genes	Relation type
LINC00664	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11085450	0.83[ASN][1000 genomes]
rs11666680	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11667259	0.86[ASN][1000 genomes]
rs11669043	0.83[ASN][1000 genomes]
rs11669130	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11671265	0.86[ASN][1000 genomes]
rs12609768	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12609823	0.87[ASN][1000 genomes]
rs12610154	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12974329	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2133822	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28498118	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28898308	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34497957	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35782355	0.82[AMR][1000 genomes]
rs35994743	0.86[ASN][1000 genomes]
rs3973190	0.87[ASN][1000 genomes]
rs4306654	0.81[ASN][1000 genomes]
rs4462731	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56346453	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511255	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6511259	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7245729	0.86[ASN][1000 genomes]
rs7246883	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7247060	0.87[ASN][1000 genomes]
rs7248989	0.83[ASN][1000 genomes]
rs7250360	0.82[AMR][1000 genomes]
rs7250838	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251082	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7251620	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7252254	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7253886	0.83[ASN][1000 genomes]
rs7256389	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7257186	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7259317	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73017722	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8101089	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8101900	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8106840	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8110814	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8111549	0.80[ASN][1000 genomes]
rs924487	0.87[ASN][1000 genomes]
rs951162	0.86[ASN][1000 genomes]
rs9973240	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
6	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
7	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
8	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs11668682	RP11-678G14.2	cis	Whole Blood	GTEx
rs11668682	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs11668682	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs11668682	CTD-2561J22.5	cis	lung	GTEx
rs11668682	RP11-678G14.2	cis	Thyroid	GTEx
rs11668682	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11668682	RP11-678G14.2	cis	Artery Tibial	GTEx
rs11668682	ZNF429	cis	Whole Blood	GTEx
rs11668682	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs11668682	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs11668682	ZNF100	cis	Muscle Skeletal	GTEx
rs11668682	ZNF429	cis	Muscle Skeletal	GTEx
rs11668682	CTD-2561J22.5	cis	Thyroid	GTEx
rs11668682	RP11-678G14.2	cis	lung	GTEx
rs11668682	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs11668682	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs11668682	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs11668682	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs11668682	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11668682	RP11-678G14.3	cis	Whole Blood	GTEx
rs11668682	RP11-420K14.2	cis	Whole Blood	GTEx
rs11668682	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs11668682	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs11668682	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs11668682	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs11668682	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs11668682	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11668682	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs11668682	RP11-678G14.3	cis	lung	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21658200-21667400	Weak transcription	Right Atrium	heart
2	chr19:21658200-21687800	Weak transcription	Brain Substantia Nigra	brain
3	chr19:21659200-21668400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:21665400-21666400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:21665600-21666200	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr19:21665600-21666400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:21665600-21666400	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr19:21665600-21666800	Active TSS	Osteobl	bone
9	chr19:21665600-21667000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
10	chr19:21665800-21666200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr19:21665800-21666200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
12	chr19:21665800-21666200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
13	chr19:21665800-21666200	Enhancers	Primary B cells from peripheral blood	blood
14	chr19:21665800-21666200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:21665800-21666200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr19:21665800-21666200	ZNF genes & repeats	Colonic Mucosa	Colon
17	chr19:21665800-21666200	ZNF genes & repeats	Gastric	stomach
18	chr19:21665800-21666200	Enhancers	Left Ventricle	heart
19	chr19:21665800-21666200	Active TSS	Psoas Muscle	Psoas
20	chr19:21665800-21666200	Active TSS	Right Ventricle	heart
21	chr19:21665800-21666200	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr19:21665800-21666200	ZNF genes & repeats	Spleen	Spleen
23	chr19:21665800-21666400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:21665800-21666400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr19:21665800-21666400	Active TSS	Colon Smooth Muscle	Colon
26	chr19:21665800-21666400	Active TSS	Rectal Smooth Muscle	rectum
27	chr19:21665800-21666600	ZNF genes & repeats	Thymus	Thymus
28	chr19:21665800-21666800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:21665800-21666800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
30	chr19:21665800-21666800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr19:21665800-21666800	Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr19:21665800-21666800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr19:21665800-21666800	Flanking Active TSS	Placenta	Placenta
34	chr19:21665800-21666800	ZNF genes & repeats	Lung	lung
35	chr19:21665800-21666800	Active TSS	Ovary	ovary
36	chr19:21665800-21667000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:21665800-21667000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:21666000-21666200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:21666000-21666200	Active TSS	Adipose Nuclei	Adipose
40	chr19:21666000-21666800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:21666000-21666800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:21666000-21666800	ZNF genes & repeats	Brain Germinal Matrix	brain
43	chr19:21666000-21666800	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr19:21666000-21668600	Weak transcription	Stomach Mucosa	stomach

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