Variant report

Variant	rs7253559
Chromosome Location	chr19:21740602-21740603
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21687245..21689707-chr19:21740240..21743085,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197013	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11085456	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11666680	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12461802	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12610154	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12973084	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12974329	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12985995	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1401926	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879237	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879238	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2133822	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2562496	0.85[AFR][1000 genomes]
rs28898308	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34040704	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34497957	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35782355	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4462731	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4611587	0.90[AFR][1000 genomes]
rs6511255	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7250360	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7251540	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7251669	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7252254	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7256389	0.82[AMR][1000 genomes]
rs7257186	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73017722	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8101089	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8101900	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8106840	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8109536	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110459	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8110814	0.81[ASN][1000 genomes]
rs8111885	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9789284	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
6	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
7	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
8	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv543942	chr19:21711611-21767567	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv543943	chr19:21713945-21759080	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv543944	chr19:21713945-21767567	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv543945	chr19:21717518-21767567	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs7253559	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs7253559	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs7253559	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs7253559	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs7253559	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7253559	RP11-678G14.3	cis	Whole Blood	GTEx
rs7253559	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs7253559	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs7253559	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs7253559	CTD-2561J22.5	cis	lung	GTEx
rs7253559	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs7253559	RP11-678G14.2	cis	Whole Blood	GTEx
rs7253559	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7253559	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs7253559	ZNF429	cis	Muscle Skeletal	GTEx
rs7253559	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7253559	RP11-678G14.3	cis	lung	GTEx
rs7253559	RP11-420K14.2	cis	Whole Blood	GTEx
rs7253559	RP11-678G14.2	cis	lung	GTEx
rs7253559	ZNF429	cis	Whole Blood	GTEx
rs7253559	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs7253559	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs7253559	RP11-678G14.2	cis	Thyroid	GTEx
rs7253559	ZNF100	cis	Muscle Skeletal	GTEx
rs7253559	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs7253559	CTD-2561J22.5	cis	Thyroid	GTEx
rs7253559	RP11-678G14.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21720400-21740800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr19:21726400-21740800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:21726600-21740800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:21735800-21741600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:21735800-21744800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:21736200-21741400	ZNF genes & repeats	Liver	Liver
7	chr19:21736400-21743000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:21737200-21743000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:21737200-21747200	ZNF genes & repeats	Fetal Intestine Small	intestine
10	chr19:21738000-21749400	Weak transcription	Left Ventricle	heart
11	chr19:21738000-21751400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:21738600-21742400	Weak transcription	Right Ventricle	heart
13	chr19:21738600-21751600	Weak transcription	Osteobl	bone
14	chr19:21738800-21740800	Weak transcription	Thymus	Thymus
15	chr19:21738800-21741200	Weak transcription	Aorta	Aorta
16	chr19:21738800-21742200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:21738800-21746000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr19:21738800-21746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:21739000-21742800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:21739200-21741000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr19:21739400-21740800	Weak transcription	Primary T cells from cord blood	blood
22	chr19:21739400-21742400	Weak transcription	Brain Hippocampus Middle	brain
23	chr19:21739400-21742400	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:21739400-21751200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr19:21739600-21741000	Weak transcription	Fetal Stomach	stomach
26	chr19:21740000-21741600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
27	chr19:21740200-21741000	ZNF genes & repeats	Ovary	ovary
28	chr19:21740200-21741200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:21740200-21741200	Strong transcription	Fetal Kidney	kidney
30	chr19:21740200-21743000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
31	chr19:21740200-21746400	ZNF genes & repeats	Fetal Intestine Large	intestine
32	chr19:21740400-21741400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
33	chr19:21740600-21741200	Strong transcription	Dnd41	blood
34	chr19:21740600-21743000	ZNF genes & repeats	Fetal Lung	lung
35	chr19:21740600-21750600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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