Variant report

Variant	rs8109757
Chromosome Location	chr19:21780307-21780308
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	CEBPB	chr19:21779625-21780840	HepG2	liver:	n/a	n/a
2	CEBPB	chr19:21778754-21780344	K562	blood:	n/a	chr19:21779166-21779177
3	CEBPB	chr19:21779688-21780694	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21780063..21781970-chr19:21783251..21784988,3	K562	blood:

Variant related genes	Relation type
ENSG00000268240	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 40 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10854054	0.83[ASN][1000 genomes]
rs11085469	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11667151	0.86[ASN][1000 genomes]
rs11879044	0.94[ASN][1000 genomes]
rs11881160	0.81[ASN][1000 genomes]
rs11881176	0.81[ASN][1000 genomes]
rs12327638	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs12459715	0.85[ASN][1000 genomes]
rs12608625	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12610221	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12972148	0.94[ASN][1000 genomes]
rs12973203	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12973209	0.85[ASN][1000 genomes]
rs12974817	0.94[ASN][1000 genomes]
rs12978060	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap]
rs12979255	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12981277	0.87[ASN][1000 genomes]
rs1520068	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1520069	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1520070	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1533674	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1850937	0.85[ASN][1000 genomes]
rs2102920	0.94[ASN][1000 genomes]
rs2102922	0.85[ASN][1000 genomes]
rs2139530	0.85[ASN][1000 genomes]
rs2359157	0.85[ASN][1000 genomes]
rs34692125	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34835488	0.94[ASN][1000 genomes]
rs35092215	0.83[ASN][1000 genomes]
rs35229762	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35465051	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35998933	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3817397	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4809140	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4809141	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4809146	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4809147	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809148	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4809151	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4809152	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4809153	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55778393	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57229007	0.84[ASN][1000 genomes]
rs59054166	0.94[ASN][1000 genomes]
rs61137407	0.84[ASN][1000 genomes]
rs62110244	0.94[ASN][1000 genomes]
rs62110249	0.84[ASN][1000 genomes]
rs6511268	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs6511273	0.85[ASN][1000 genomes]
rs67854708	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67876192	0.81[EUR][1000 genomes]
rs7246154	0.85[ASN][1000 genomes]
rs7248367	0.85[ASN][1000 genomes]
rs7250457	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250470	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250663	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250960	0.86[ASN][1000 genomes]
rs7251111	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254018	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254378	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7255081	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257246	0.85[ASN][1000 genomes]
rs7260514	0.85[ASN][1000 genomes]
rs8110320	0.85[ASN][1000 genomes]
rs8111076	0.85[ASN][1000 genomes]
rs8111313	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8112158	0.85[ASN][1000 genomes]
rs8112960	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9749033	0.85[ASN][1000 genomes]
rs9749043	0.85[ASN][1000 genomes]
rs9749067	0.85[ASN][1000 genomes]
rs9749163	0.85[ASN][1000 genomes]
rs9749167	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1056332	chr19:21746555-21807647	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv960938	chr19:21766627-21785276	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:40)

SNP	Gene	Cis/trans	Tissue	Source
rs8109757	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs8109757	RP11-678G14.2	cis	Thyroid	GTEx
rs8109757	LINC00664	cis	lung	GTEx
rs8109757	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs8109757	ZNF100	cis	Muscle Skeletal	GTEx
rs8109757	CTD-2561J22.5	cis	Thyroid	GTEx
rs8109757	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs8109757	RP11-678G14.3	cis	Whole Blood	GTEx
rs8109757	ZNF493	cis	Esophagus Mucosa	GTEx
rs8109757	ZNF429	cis	Whole Blood	GTEx
rs8109757	RP11-678G14.3	cis	Thyroid	GTEx
rs8109757	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs8109757	RP11-678G14.3	cis	Stomach	GTEx
rs8109757	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs8109757	ZNF708	cis	Whole Blood	GTEx
rs8109757	ZNF429	cis	Artery Tibial	GTEx
rs8109757	CTD-2561J22.5	cis	Whole Blood	GTEx
rs8109757	ZNF429	cis	lung	GTEx
rs8109757	ZNF429	cis	Muscle Skeletal	GTEx
rs8109757	ZNF493	cis	Whole Blood	GTEx
rs8109757	RP11-678G14.2	cis	lung	GTEx
rs8109757	LOC400680	Cis_1M	lymphoblastoid	RTeQTL
rs8109757	RP11-678G14.2	cis	Artery Tibial	GTEx
rs8109757	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs8109757	RP11-420K14.2	cis	Whole Blood	GTEx
rs8109757	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs8109757	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs8109757	LINC00664	cis	Muscle Skeletal	GTEx
rs8109757	RP11-420K14.2	cis	lung	GTEx
rs8109757	ZNF429	cis	Esophagus Mucosa	GTEx
rs8109757	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs8109757	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs8109757	RP11-678G14.3	cis	Esophagus Mucosa	GTEx
rs8109757	LINC00664	cis	Whole Blood	GTEx
rs8109757	RP11-678G14.2	cis	Whole Blood	GTEx
rs8109757	RP11-678G14.3	cis	lung	GTEx
rs8109757	ZNF43	cis	Esophagus Mucosa	GTEx
rs8109757	RP11-678G14.4	cis	Muscle Skeletal	GTEx
rs8109757	CTD-2561J22.5	cis	Esophagus Mucosa	GTEx
rs8109757	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21770000-21786600	Weak transcription	Primary T cells from cord blood	blood
2	chr19:21770200-21786600	Weak transcription	Right Ventricle	heart
3	chr19:21771000-21786200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:21771200-21786200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:21771200-21786200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr19:21771400-21782200	Weak transcription	Fetal Intestine Large	intestine
7	chr19:21771400-21785000	Weak transcription	Fetal Intestine Small	intestine
8	chr19:21777600-21781400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:21778000-21783600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr19:21778200-21782000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:21778200-21785800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr19:21778800-21781000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
13	chr19:21779200-21780600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:21779400-21780600	Genic enhancers	Pancreas	Pancrea
15	chr19:21779400-21780600	ZNF genes & repeats	K562	blood
16	chr19:21779600-21780800	Strong transcription	Dnd41	blood
17	chr19:21780000-21782600	Weak transcription	H1 Cell Line	embryonic stem cell

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