Variant report

Variant	rs28839521
Chromosome Location	chr19:21599000-21599001
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	chr19:21596819..21599115-chr19:21600673..21603133,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11673406	0.82[EUR][1000 genomes]
rs12150996	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12151067	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151068	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151222	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12971724	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975330	0.80[ASN][1000 genomes]
rs12975981	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12976011	0.80[ASN][1000 genomes]
rs12981869	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12984238	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566474	0.80[ASN][1000 genomes]
rs1566476	0.80[ASN][1000 genomes]
rs1566477	0.80[ASN][1000 genomes]
rs16997924	0.80[ASN][1000 genomes]
rs17618715	0.80[ASN][1000 genomes]
rs17618778	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1762580	0.80[ASN][1000 genomes]
rs2262897	0.80[ASN][1000 genomes]
rs2562457	0.80[ASN][1000 genomes]
rs2562458	0.80[ASN][1000 genomes]
rs2562459	0.80[ASN][1000 genomes]
rs2650778	0.80[ASN][1000 genomes]
rs2650780	0.80[ASN][1000 genomes]
rs2650781	0.80[ASN][1000 genomes]
rs2650782	0.80[ASN][1000 genomes]
rs2650783	0.80[ASN][1000 genomes]
rs2650785	0.80[ASN][1000 genomes]
rs2650786	0.80[ASN][1000 genomes]
rs2650808	0.80[ASN][1000 genomes]
rs2650810	0.82[EUR][1000 genomes]
rs28875571	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2914629	0.82[EUR][1000 genomes]
rs2914636	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2914637	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2914647	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2928210	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2968081	0.80[ASN][1000 genomes]
rs34560125	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34875588	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35148123	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35245030	0.80[ASN][1000 genomes]
rs35578515	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35860067	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4332859	0.80[ASN][1000 genomes]
rs4341872	0.81[EUR][1000 genomes]
rs4461198	0.81[EUR][1000 genomes]
rs483383	0.80[ASN][1000 genomes]
rs501647	0.80[ASN][1000 genomes]
rs509540	0.80[ASN][1000 genomes]
rs514390	0.80[AMR][1000 genomes]
rs549882	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs552039	0.80[ASN][1000 genomes]
rs56152627	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs566230	0.80[ASN][1000 genomes]
rs57055133	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57841525	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58121117	0.80[ASN][1000 genomes]
rs59617671	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs608002	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62107470	0.80[ASN][1000 genomes]
rs62107538	0.80[ASN][1000 genomes]
rs62109224	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62110379	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62111469	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62111470	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62111472	0.80[ASN][1000 genomes]
rs62111476	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6511247	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs670813	0.80[ASN][1000 genomes]
rs67723811	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685844	0.80[ASN][1000 genomes]
rs7245848	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7246684	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7248700	0.83[AMR][1000 genomes]
rs7257584	0.86[ASN][1000 genomes]
rs7258211	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7258523	0.83[ASN][1000 genomes]
rs7259178	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73025767	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8099863	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8101077	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8101442	0.80[ASN][1000 genomes]
rs8102655	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8103151	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8103417	0.81[EUR][1000 genomes]
rs8105404	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8105629	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107940	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8111189	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8112359	0.83[ASN][1000 genomes]
rs8113558	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
15	nsv578953	chr19:21586797-21609607	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
16	nsv578954	chr19:21587261-21604510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28839521	ZNF738	cis	Thyroid	GTEx
rs28839521	ZNF429	cis	Whole Blood	GTEx
rs28839521	ZNF429	cis	Artery Aorta	GTEx
rs28839521	ZNF738	cis	Adipose Subcutaneous	GTEx
rs28839521	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs28839521	ZNF493	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21580600-21600200	Weak transcription	Gastric	stomach
2	chr19:21580600-21602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:21581600-21601800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:21581800-21607000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:21586000-21599400	Weak transcription	Spleen	Spleen
7	chr19:21590000-21600200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:21590200-21606400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:21590600-21608200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
10	chr19:21590800-21601200	Strong transcription	Ovary	ovary
11	chr19:21591600-21599000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr19:21591800-21607000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
13	chr19:21592800-21601200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr19:21593200-21602400	Weak transcription	HSMM	muscle
15	chr19:21593400-21610200	ZNF genes & repeats	Liver	Liver
16	chr19:21593600-21606600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:21594000-21600400	Strong transcription	Left Ventricle	heart
18	chr19:21594200-21601200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:21595000-21599800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:21595000-21601400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:21595400-21601200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr19:21595400-21601400	Strong transcription	Fetal Intestine Large	intestine
23	chr19:21595600-21599200	Strong transcription	Brain Germinal Matrix	brain
24	chr19:21596600-21599600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:21596600-21599600	Weak transcription	Fetal Stomach	stomach
26	chr19:21596600-21600200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:21596600-21600800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:21596800-21599600	Weak transcription	Fetal Intestine Small	intestine
29	chr19:21596800-21601200	Weak transcription	Fetal Muscle Leg	muscle
30	chr19:21597000-21599600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:21597000-21600800	Weak transcription	Pancreas	Pancrea
32	chr19:21597000-21601000	Weak transcription	Placenta	Placenta
33	chr19:21597000-21601200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:21597000-21602200	Weak transcription	HSMMtube	muscle
35	chr19:21597200-21599600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:21597200-21599600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:21597200-21599600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr19:21597200-21600000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:21597200-21600000	Weak transcription	Brain Substantia Nigra	brain
40	chr19:21597200-21600000	Weak transcription	Fetal Lung	lung
41	chr19:21597200-21600400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr19:21597200-21600400	Weak transcription	Lung	lung
43	chr19:21597200-21601200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:21597200-21601800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr19:21597200-21602400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:21597400-21599200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:21597400-21599600	Weak transcription	Thymus	Thymus
48	chr19:21597600-21599200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr19:21597600-21599200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:21597600-21599400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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