Variant report

Variant	rs11667259
Chromosome Location	chr19:21639989-21639990
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21637958..21640581-chr19:21645162..21647289,2	K562	blood:

Variant related genes	Relation type
ENSG00000268119	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10405716	0.83[EUR][1000 genomes]
rs1055753	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11085450	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11666680	0.81[ASN][1000 genomes]
rs11667770	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11668682	0.86[ASN][1000 genomes]
rs11668691	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11669043	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11669130	0.87[ASN][1000 genomes]
rs11671265	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12609823	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12610154	0.81[ASN][1000 genomes]
rs12979646	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12983787	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2133819	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2133822	0.81[ASN][1000 genomes]
rs2650774	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28498118	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34152818	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35773446	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35994743	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3973190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4306654	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4621113	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56346453	0.88[ASN][1000 genomes]
rs6511237	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6511238	0.82[EUR][1000 genomes]
rs6511239	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6511242	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6511245	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6511246	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7245729	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7246883	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7247060	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7248989	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7249412	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7251620	0.82[ASN][1000 genomes]
rs7252254	0.81[ASN][1000 genomes]
rs7253886	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7254059	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7257857	0.81[AMR][1000 genomes]
rs7259311	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8101089	0.81[ASN][1000 genomes]
rs8111549	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs924487	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs951162	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9973240	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv961284	chr19:21636687-21659271	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs11667259	RP11-678G14.2	cis	lung	GTEx
rs11667259	RP11-678G14.2	cis	Nerve Tibial	GTEx
rs11667259	RP11-678G14.2	cis	Artery Tibial	GTEx
rs11667259	CTD-2561J22.5	cis	Thyroid	GTEx
rs11667259	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs11667259	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11667259	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs11667259	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs11667259	RP11-678G14.3	cis	lung	GTEx
rs11667259	RP11-678G14.2	cis	Thyroid	GTEx
rs11667259	ZNF493	cis	Heart Left Ventricle	GTEx
rs11667259	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs11667259	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11667259	ZNF429	cis	Whole Blood	GTEx
rs11667259	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs11667259	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs11667259	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs11667259	LINC00664	cis	Adipose Subcutaneous	GTEx
rs11667259	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs11667259	RP11-678G14.2	cis	Whole Blood	GTEx
rs11667259	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs11667259	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs11667259	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs11667259	CTD-2561J22.5	cis	lung	GTEx
rs11667259	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs11667259	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs11667259	ZNF429	cis	Muscle Skeletal	GTEx
rs11667259	RP11-420K14.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21629800-21641400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
2	chr19:21630000-21642000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
3	chr19:21630200-21643800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:21630400-21643800	ZNF genes & repeats	Dnd41	blood
5	chr19:21633800-21641400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:21633800-21641400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:21634600-21641600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:21635600-21642000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
9	chr19:21635600-21642000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr19:21635800-21641200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr19:21636200-21641000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
12	chr19:21636800-21640000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
13	chr19:21636800-21641400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr19:21636800-21645800	Weak transcription	Fetal Kidney	kidney
15	chr19:21636800-21646200	Weak transcription	Fetal Heart	heart
16	chr19:21637200-21641000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr19:21638200-21640600	Weak transcription	Ovary	ovary
18	chr19:21638200-21642800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:21638400-21640600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:21638800-21640600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:21638800-21642600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:21639200-21641400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:21639400-21640400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:21639400-21640400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr19:21639400-21640400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:21639400-21645600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:21639600-21640400	Weak transcription	Fetal Lung	lung
28	chr19:21639600-21642000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:21639600-21646000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:21639800-21640400	Enhancers	K562	blood
31	chr19:21639800-21641600	ZNF genes & repeats	Fetal Intestine Small	intestine

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