Variant report

Variant	rs55743020
Chromosome Location	chr19:38188233-38188234
allele	G/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	POLR2A	chr19:38188219-38188340	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr19:38188197-38188305	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:38187852-38188371	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:38188142-38188252	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:38188103-38188297	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38134173..38137861-chr19:38186479..38189500,3	K562	blood:

Variant related genes	Relation type
ZFP30	TF binding region
ENSG00000267319	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10445548	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1048505	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061753	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061756	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12150862	0.91[ASN][1000 genomes]
rs12151082	0.91[ASN][1000 genomes]
rs12151156	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244713	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244769	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17248097	0.91[ASN][1000 genomes]
rs17248670	0.91[ASN][1000 genomes]
rs17249138	0.91[ASN][1000 genomes]
rs17303902	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17304703	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305193	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305228	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305823	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17306900	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1871196	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291001	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306201	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2385005	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35153242	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3859549	0.91[ASN][1000 genomes]
rs4536583	0.91[ASN][1000 genomes]
rs55681348	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55718806	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55865869	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55909413	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56184201	0.91[ASN][1000 genomes]
rs56233644	0.91[ASN][1000 genomes]
rs56268127	0.91[ASN][1000 genomes]
rs56277404	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56290614	0.91[ASN][1000 genomes]
rs56351266	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57654288	0.97[EUR][1000 genomes]
rs57943942	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62108291	0.82[EUR][1000 genomes]
rs62108306	0.84[EUR][1000 genomes]
rs7245855	1.00[ASN][1000 genomes]
rs7259272	0.84[EUR][1000 genomes]
rs73031330	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033122	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033134	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033142	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73035159	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73035160	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73039029	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041006	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73041036	0.91[ASN][1000 genomes]
rs8101610	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104282	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104994	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8108268	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110293	0.91[ASN][1000 genomes]
rs8111790	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv978813	chr19:38187175-38188871	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs55743020	AC012309.5	cis	Thyroid	GTEx
rs55743020	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs55743020	AC012309.5	cis	Heart Left Ventricle	GTEx
rs55743020	AC012309.5	cis	Artery Tibial	GTEx
rs55743020	AC012309.5	cis	Esophagus Mucosa	GTEx
rs55743020	AC012309.5	cis	Esophagus Muscularis	GTEx
rs55743020	AC012309.5	cis	lung	GTEx
rs55743020	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs55743020	AC012309.5	cis	Muscle Skeletal	GTEx
rs55743020	ZNF781	cis	Thyroid	GTEx
rs55743020	ZNF781	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38183200-38208800	Weak transcription	Fetal Heart	heart
2	chr19:38183400-38188800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr19:38183400-38190000	Weak transcription	Stomach Mucosa	stomach
4	chr19:38183600-38188800	Weak transcription	Fetal Kidney	kidney
5	chr19:38183600-38189400	Weak transcription	Psoas Muscle	Psoas
6	chr19:38183600-38190000	Weak transcription	Small Intestine	intestine
7	chr19:38184200-38188600	Weak transcription	Fetal Brain Male	brain
8	chr19:38184200-38201200	Weak transcription	Colonic Mucosa	Colon
9	chr19:38184400-38208800	Weak transcription	HepG2	liver
10	chr19:38186400-38191200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
11	chr19:38186800-38189200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:38186800-38189800	Strong transcription	Fetal Stomach	stomach
13	chr19:38186800-38191200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:38187200-38190800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:38187200-38191600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:38187400-38188400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:38187400-38188400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:38187400-38188400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:38187400-38188400	ZNF genes & repeats	Aorta	Aorta
22	chr19:38187400-38188400	ZNF genes & repeats	Esophagus	oesophagus
23	chr19:38187400-38188400	Strong transcription	Fetal Intestine Small	intestine
24	chr19:38187400-38188400	ZNF genes & repeats	Gastric	stomach
25	chr19:38187400-38188400	ZNF genes & repeats	Lung	lung
26	chr19:38187400-38188400	ZNF genes & repeats	Ovary	ovary
27	chr19:38187400-38188400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr19:38187400-38188600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
29	chr19:38187400-38188600	Strong transcription	Brain Substantia Nigra	brain
30	chr19:38187400-38189000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:38187400-38189200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
32	chr19:38187400-38189800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:38187400-38190400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:38187400-38190600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:38187400-38190600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr19:38187400-38190600	Strong transcription	Fetal Brain Female	brain
37	chr19:38187400-38190800	ZNF genes & repeats	Adipose Nuclei	Adipose
38	chr19:38187400-38190800	Strong transcription	Brain Angular Gyrus	brain
39	chr19:38187400-38190800	Strong transcription	Brain Germinal Matrix	brain
40	chr19:38187400-38190800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:38187400-38190800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
42	chr19:38187400-38190800	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr19:38187400-38190800	ZNF genes & repeats	HSMM	muscle
44	chr19:38187400-38190800	ZNF genes & repeats	NHLF	lung
45	chr19:38187400-38191000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
46	chr19:38187400-38191000	Strong transcription	Brain Anterior Caudate	brain
47	chr19:38187400-38191000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr19:38187400-38191200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:38187400-38191400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:38187400-38191400	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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