Variant report

Variant	rs57055133
Chromosome Location	chr19:21550330-21550331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs11671832	0.82[ASN][1000 genomes]
rs12151067	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12151068	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12971724	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12975981	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12981869	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12984238	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1678822	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17618715	1.00[ASN][1000 genomes]
rs17618778	0.80[ASN][1000 genomes]
rs1762580	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680671	0.89[ASN][1000 genomes]
rs1827225	0.86[ASN][1000 genomes]
rs2358984	0.83[EUR][1000 genomes]
rs28839521	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2914636	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914637	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928210	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34560125	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34875588	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35148123	0.80[ASN][1000 genomes]
rs35578515	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35860067	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs483383	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488125	0.87[EUR][1000 genomes]
rs501647	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504280	0.87[EUR][1000 genomes]
rs509540	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514390	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs531283	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs549882	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552039	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565406	0.82[EUR][1000 genomes]
rs566230	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58121117	1.00[ASN][1000 genomes]
rs59617671	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608002	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617186	0.86[EUR][1000 genomes]
rs62107470	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107538	1.00[ASN][1000 genomes]
rs62109224	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110379	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635730	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6511228	0.83[EUR][1000 genomes]
rs670813	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67723811	0.80[ASN][1000 genomes]
rs685844	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245848	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246684	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248700	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252873	0.83[EUR][1000 genomes]
rs7254762	0.89[ASN][1000 genomes]
rs7258086	0.83[EUR][1000 genomes]
rs73025767	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099863	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102328	0.83[EUR][1000 genomes]
rs8103411	0.85[ASN][1000 genomes]
rs8103417	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8105404	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110470	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8111189	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113558	0.83[AMR][1000 genomes];0.85[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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs57055133	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs57055133	ZNF738	cis	Nerve Tibial	GTEx
rs57055133	CTD-2561J22.5	cis	Thyroid	GTEx
rs57055133	ZNF738	cis	Thyroid	GTEx
rs57055133	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs57055133	ZNF738	cis	Adipose Subcutaneous	GTEx
rs57055133	ZNF429	cis	Whole Blood	GTEx
rs57055133	ZNF738	cis	Esophagus Muscularis	GTEx
rs57055133	ZNF738	cis	Artery Tibial	GTEx
rs57055133	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21542400-21550400	Weak transcription	Lung	lung
2	chr19:21542400-21555400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr19:21542400-21555400	Weak transcription	Psoas Muscle	Psoas
4	chr19:21542400-21555600	Weak transcription	Colonic Mucosa	Colon
5	chr19:21542400-21557800	Weak transcription	Gastric	stomach
6	chr19:21542400-21562200	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:21542400-21562200	Weak transcription	Fetal Heart	heart
8	chr19:21542400-21563200	Weak transcription	Brain Substantia Nigra	brain
9	chr19:21542600-21550400	Weak transcription	Esophagus	oesophagus
10	chr19:21542600-21550400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr19:21542600-21550400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr19:21542600-21555000	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:21542600-21555000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr19:21542600-21555000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr19:21542600-21555200	Weak transcription	Brain Anterior Caudate	brain
16	chr19:21542600-21555600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:21542600-21561400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:21542600-21561400	Weak transcription	Pancreas	Pancrea
19	chr19:21542800-21550400	Weak transcription	Aorta	Aorta
20	chr19:21542800-21555000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:21542800-21561400	Weak transcription	Right Ventricle	heart
22	chr19:21543000-21550400	Weak transcription	Brain Angular Gyrus	brain
23	chr19:21543000-21553200	Weak transcription	Osteobl	bone
24	chr19:21543000-21555600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr19:21543000-21556600	Weak transcription	HepG2	liver
26	chr19:21543000-21563000	Weak transcription	NHLF	lung
27	chr19:21543000-21566600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:21543000-21566800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:21543200-21555200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
30	chr19:21543200-21555400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:21543200-21555800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr19:21543200-21556600	ZNF genes & repeats	GM12878-XiMat	blood
33	chr19:21543200-21557000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:21543400-21552000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:21543400-21552800	Strong transcription	Fetal Muscle Leg	muscle
36	chr19:21543400-21555400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:21543400-21560000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr19:21543400-21560400	ZNF genes & repeats	Fetal Brain Female	brain
39	chr19:21543400-21566400	ZNF genes & repeats	Brain Germinal Matrix	brain
40	chr19:21543400-21570600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr19:21543600-21555000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr19:21543600-21563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:21543600-21566400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:21543800-21551400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr19:21543800-21552000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr19:21543800-21556800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:21543800-21566600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:21543800-21567400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:21544000-21551600	Weak transcription	Small Intestine	intestine
50	chr19:21544200-21551200	Strong transcription	Fetal Muscle Trunk	muscle

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