Variant report

Variant	rs2972554
Chromosome Location	chr19:36747940-36747941
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11672641	0.98[ASN][1000 genomes]
rs1898675	0.82[ASN][1000 genomes]
rs2918323	0.85[ASN][1000 genomes]
rs2918324	0.87[ASN][1000 genomes]
rs2918325	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2918328	0.93[ASN][1000 genomes]
rs2918329	0.88[ASN][1000 genomes]
rs2918330	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2918331	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2918334	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2918355	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2918356	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2918358	0.85[ASN][1000 genomes]
rs2918382	0.81[ASN][1000 genomes]
rs2972528	0.93[ASN][1000 genomes]
rs2972530	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2972532	0.86[ASN][1000 genomes]
rs2972536	0.81[ASN][1000 genomes]
rs2972548	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972550	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972551	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4805169	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4805170	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4806289	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4806291	0.98[ASN][1000 genomes]
rs4806292	0.80[EUR][1000 genomes]
rs7254149	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7255170	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9797716	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv9715	chr19:36729688-36811749	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1063208	chr19:36743461-36847486	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv961212	chr19:36744378-36801298	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv960831	chr19:36744378-36813769	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2972554	ZNF545	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36730400-36748400	Weak transcription	HSMMtube	muscle
2	chr19:36737400-36748000	Weak transcription	Ovary	ovary
3	chr19:36739600-36756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:36744800-36748000	ZNF genes & repeats	Fetal Brain Female	brain
5	chr19:36745400-36748000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
6	chr19:36745400-36749200	ZNF genes & repeats	Pancreas	Pancrea
7	chr19:36745800-36750600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr19:36746200-36748200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
9	chr19:36746200-36748800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:36746200-36749400	ZNF genes & repeats	Fetal Stomach	stomach
11	chr19:36746400-36748800	ZNF genes & repeats	Spleen	Spleen
12	chr19:36746800-36748000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:36746800-36748000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr19:36747000-36750000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:36747400-36748000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:36747600-36749200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:36747600-36749200	Enhancers	Fetal Brain Male	brain
18	chr19:36747600-36749400	ZNF genes & repeats	Lung	lung
19	chr19:36747800-36748000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:36747800-36748000	Active TSS	Adipose Nuclei	Adipose
21	chr19:36747800-36748000	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr19:36747800-36748000	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr19:36747800-36748000	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr19:36747800-36748000	Enhancers	Fetal Muscle Leg	muscle
25	chr19:36747800-36748000	Enhancers	Right Ventricle	heart
26	chr19:36747800-36748200	ZNF genes & repeats	Brain Germinal Matrix	brain
27	chr19:36747800-36748200	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr19:36747800-36748200	Flanking Active TSS	Fetal Muscle Trunk	muscle
29	chr19:36747800-36748600	ZNF genes & repeats	Colonic Mucosa	Colon
30	chr19:36747800-36748800	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr19:36747800-36748800	Active TSS	Brain Angular Gyrus	brain
32	chr19:36747800-36749000	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr19:36747800-36749000	Active TSS	Brain Substantia Nigra	brain
34	chr19:36747800-36749200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr19:36747800-36749200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr19:36747800-36749200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:36747800-36749400	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr19:36747800-36749400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:36747800-36749400	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr19:36747800-36749600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
41	chr19:36747800-36749600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:36747800-36749600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr19:36747800-36749800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:36747800-36749800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin

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