Variant report

Variant	rs514390
Chromosome Location	chr19:21506719-21506720
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	chr19:21504637..21507576-chr19:21510636..21512879,2	MCF-7	breast:
2	chr19:21496090..21497696-chr19:21505089..21507534,2	K562	blood:

Variant related genes	Relation type
ENSG00000182141	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11085443	0.80[EUR][1000 genomes]
rs12151067	0.80[AMR][1000 genomes]
rs12151068	0.80[AMR][1000 genomes]
rs12975981	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12981869	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1678822	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17618715	0.95[ASN][1000 genomes]
rs1762580	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17680671	0.84[ASN][1000 genomes]
rs1781863	0.83[EUR][1000 genomes]
rs1813234	0.80[EUR][1000 genomes]
rs1827225	0.82[ASN][1000 genomes]
rs28839521	0.80[AMR][1000 genomes]
rs2914636	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2914637	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2928210	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34560125	0.80[AMR][1000 genomes]
rs34875588	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35578515	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35860067	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs483383	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488125	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs501647	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs504280	0.94[EUR][1000 genomes]
rs509540	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs531283	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs549882	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs552039	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs565406	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs566230	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57055133	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58121117	0.95[ASN][1000 genomes]
rs59617671	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs600428	0.82[EUR][1000 genomes]
rs608002	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs617186	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62107470	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62107538	0.95[ASN][1000 genomes]
rs62109224	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62110379	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs635730	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs670813	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs685844	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7245848	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7246684	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7248700	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7254762	0.84[ASN][1000 genomes]
rs73025767	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8099863	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8103411	0.81[ASN][1000 genomes]
rs8103417	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8105404	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8110470	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111189	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8113558	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv963023	chr19:21491992-21570395	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs514390	ZNF738	cis	Thyroid	GTEx
rs514390	ZNF738	cis	Esophagus Muscularis	GTEx
rs514390	ZNF738	cis	Nerve Tibial	GTEx
rs514390	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs514390	CTD-2561J22.5	cis	Thyroid	GTEx
rs514390	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs514390	ZNF738	cis	Adipose Subcutaneous	GTEx
rs514390	ZNF738	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21473800-21510400	Weak transcription	Fetal Heart	heart
2	chr19:21474800-21509800	Weak transcription	Fetal Brain Male	brain
3	chr19:21475200-21511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:21484400-21511000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:21485400-21508600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:21485400-21511200	Weak transcription	Gastric	stomach
7	chr19:21487600-21508600	Weak transcription	Fetal Kidney	kidney
8	chr19:21487600-21511200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:21488200-21511200	Weak transcription	Aorta	Aorta
10	chr19:21489000-21510800	Weak transcription	NH-A	brain
11	chr19:21489600-21509000	Weak transcription	Placenta	Placenta
12	chr19:21490200-21508800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:21490200-21509200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:21492400-21508600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:21492400-21508800	Weak transcription	Fetal Intestine Large	intestine
16	chr19:21492400-21509000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:21492600-21509000	Weak transcription	Fetal Muscle Leg	muscle
18	chr19:21493000-21509200	Weak transcription	Fetal Intestine Small	intestine
19	chr19:21495400-21508400	Weak transcription	Fetal Brain Female	brain
20	chr19:21496800-21509800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:21497400-21508600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr19:21497600-21511000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:21498000-21506800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:21498400-21510600	Weak transcription	HUVEC	blood vessel
25	chr19:21498400-21511200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:21498800-21510400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:21500000-21509400	Weak transcription	Fetal Stomach	stomach
28	chr19:21500600-21509000	Weak transcription	Primary T cells from cord blood	blood
29	chr19:21500800-21506800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr19:21501000-21508800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr19:21501000-21508800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:21501000-21509000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:21501000-21509000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:21501000-21509000	Weak transcription	HSMM	muscle
35	chr19:21501000-21509400	Weak transcription	Esophagus	oesophagus
36	chr19:21501000-21510600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:21501000-21511200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr19:21501000-21511200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:21501000-21511200	Weak transcription	Psoas Muscle	Psoas
40	chr19:21501200-21508600	Weak transcription	A549	lung
41	chr19:21501200-21508800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr19:21501200-21510800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:21501600-21508800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:21501600-21509000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr19:21501600-21509000	Weak transcription	Dnd41	blood
46	chr19:21502200-21506800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:21502400-21508000	Enhancers	Brain Hippocampus Middle	brain
48	chr19:21502600-21506800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr19:21502800-21507600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:21503000-21508800	Weak transcription	Primary B cells from peripheral blood	blood

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