Variant report

Variant	rs1401926
Chromosome Location	chr19:21740932-21740933
allele	C/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: 75 )
Associated
traits (count: 44 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1055753	0.90[JPT][hapmap]
rs11085447	0.83[CHD][hapmap];0.95[JPT][hapmap]
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]
rs11667770	0.89[JPT][hapmap]
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]
rs12975081	0.90[JPT][hapmap]
rs12981564	0.89[JPT][hapmap]
rs12981735	0.83[JPT][hapmap]
rs12982282	0.90[JPT][hapmap]
rs12985995	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2012013	0.83[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs2088762	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2133822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2170024	0.90[JPT][hapmap]
rs2562496	0.87[AFR][1000 genomes]
rs28898308	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2914638	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs34040704	0.94[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]
rs4315457	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4462731	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4611587	0.91[AFR][1000 genomes]
rs4621113	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4809145	0.81[JPT][hapmap]
rs6511239	0.89[JPT][hapmap]
rs6511255	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7247411	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs7248601	0.83[JPT][hapmap]
rs7249412	0.90[JPT][hapmap]
rs7249636	0.81[CHD][hapmap]
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	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7253249	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7253559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256389	0.82[AMR][1000 genomes]
rs7257186	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7257857	0.81[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap]
rs7259311	0.90[JPT][hapmap]
rs73017722	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7508671	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs8099940	0.90[JPT][hapmap]
rs8101089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];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]
rs8103325	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs8103459	0.88[JPT][hapmap]
rs8106840	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8109536	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8109940	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8110459	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8110814	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs8111885	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs924487	0.94[CHB][hapmap];0.85[JPT][hapmap]
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:44)

SNP	Gene	Cis/trans	Tissue	Source
rs1401926	ZNF429	cis	cerebellum	SCAN
rs1401926	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs1401926	hCT1818887.2	cis	multi-tissue	Pritchard
rs1401926	RP11-678G14.3	cis	lung	GTEx
rs1401926	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs1401926	ZNF429	cis	Whole Blood	GTEx
rs1401926	RP11-678G14.2	cis	Whole Blood	GTEx
rs1401926	RP11-678G14.2	cis	Thyroid	GTEx
rs1401926	ZNF738	cis	multi-tissue	Pritchard
rs1401926	ZNF93	cis	cerebellum	SCAN
rs1401926	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs1401926	RP11-678G14.3	cis	Whole Blood	GTEx
rs1401926	ZNF493	cis	cerebellum	SCAN
rs1401926	CTD-2561J22.5	cis	Thyroid	GTEx
rs1401926	RP11-678G14.2	cis	lung	GTEx
rs1401926	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs1401926	Contig26081_RC	trans	multi-tissue	Pritchard
rs1401926	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs1401926	ZNF429	cis	multi-tissue	Pritchard
rs1401926	FGD6	cis	Liver	GTEx
rs1401926	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1401926	ZNF738	cis	Liver	GTEx
rs1401926	C19orf50	cis	cerebellum	SCAN
rs1401926	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs1401926	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1401926	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs1401926	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs1401926	ZNF208	cis	parietal	SCAN
rs1401926	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1401926	CTD-2561J22.5	cis	lung	GTEx
rs1401926	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs1401926	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs1401926	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs1401926	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs1401926	ZNF43	cis	parietal	SCAN
rs1401926	ZNF100	cis	Muscle Skeletal	GTEx
rs1401926	ZNF429	cis	parietal	SCAN
rs1401926	ZNF486	cis	cerebellum	SCAN
rs1401926	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs1401926	RP11-420K14.2	cis	Whole Blood	GTEx
rs1401926	ZNF708	cis	cerebellum	SCAN
rs1401926	ZNF493	cis	multi-tissue	Pritchard
rs1401926	ZNF826P	cis	parietal	SCAN
rs1401926	ZNF429	cis	Muscle Skeletal	GTEx

Chromatin state (count:40 , 50 per page) page: 1

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

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