Variant report

Variant	rs34991303
Chromosome Location	chr19:38197572-38197573
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1060522	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10853710	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083433	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11666172	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11668796	0.91[EUR][1000 genomes]
rs11671953	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11673497	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16975299	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17246792	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28431170	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2891657	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55871826	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55913702	0.91[EUR][1000 genomes]
rs55950325	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62108305	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62108351	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508739	0.91[EUR][1000 genomes]
rs7249622	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253081	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258385	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73037060	0.88[EUR][1000 genomes];0.89[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	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34991303	ZNF573	cis	multi-tissue	Pritchard
rs34991303	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:118 , 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	chr19:38184200-38201200	Weak transcription	Colonic Mucosa	Colon
3	chr19:38184400-38208800	Weak transcription	HepG2	liver
4	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38187400-38199000	ZNF genes & repeats	A549	lung
7	chr19:38187400-38205800	Strong transcription	Dnd41	blood
8	chr19:38187400-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:38188000-38198200	Weak transcription	Pancreas	Pancrea
10	chr19:38188200-38197800	Weak transcription	Right Ventricle	heart
11	chr19:38188200-38209200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:38188400-38202000	Weak transcription	Placenta	Placenta
13	chr19:38189400-38209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:38190000-38206600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:38190600-38198000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:38190600-38198400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:38190600-38198400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:38190600-38209000	Weak transcription	Brain Substantia Nigra	brain
19	chr19:38190600-38209200	Weak transcription	HSMMtube	muscle
20	chr19:38190800-38198200	Weak transcription	Brain Angular Gyrus	brain
21	chr19:38190800-38198200	Weak transcription	Osteobl	bone
22	chr19:38190800-38198600	Weak transcription	HSMM	muscle
23	chr19:38190800-38202200	Weak transcription	NH-A	brain
24	chr19:38190800-38209000	Weak transcription	Stomach Mucosa	stomach
25	chr19:38190800-38209200	Weak transcription	Fetal Thymus	thymus
26	chr19:38190800-38209200	Weak transcription	Psoas Muscle	Psoas
27	chr19:38191000-38197600	Weak transcription	Brain Anterior Caudate	brain
28	chr19:38191000-38197800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr19:38191000-38197800	Weak transcription	Fetal Brain Male	brain
30	chr19:38191000-38198000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:38191200-38198400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr19:38191200-38209200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr19:38191200-38209200	Weak transcription	Colon Smooth Muscle	Colon
34	chr19:38191600-38202000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:38192200-38203000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:38192600-38198200	Weak transcription	Aorta	Aorta
37	chr19:38192600-38198400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr19:38193800-38209000	Weak transcription	Hela-S3	cervix
39	chr19:38194000-38203000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:38194200-38197800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
41	chr19:38194200-38202800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:38194600-38198400	Weak transcription	NHEK	skin
43	chr19:38194600-38198800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:38194600-38206600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:38194800-38200400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:38195000-38197800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:38195200-38204400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr19:38195400-38199000	Strong transcription	Adipose Nuclei	Adipose
49	chr19:38195400-38199200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
50	chr19:38195600-38198400	Strong transcription	Ovary	ovary

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