Variant report

Variant	rs11666172
Chromosome Location	chr19:38205764-38205765
allele	C/T
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	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853710	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083433	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11668796	0.90[EUR][1000 genomes]
rs11671953	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11673497	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16975299	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17246792	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28431170	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2891657	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34991303	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55871826	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55913702	0.90[EUR][1000 genomes]
rs55950325	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108305	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62108351	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508739	0.90[EUR][1000 genomes]
rs7249622	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253081	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258385	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73037060	0.86[EUR][1000 genomes];0.81[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
rs11666172	ZNF573	cis	multi-tissue	Pritchard
rs11666172	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:108 , 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	chr19:38184400-38208800	Weak transcription	HepG2	liver
3	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:38187400-38205800	Strong transcription	Dnd41	blood
6	chr19:38187400-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:38188200-38209200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38189400-38209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:38190000-38206600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:38190600-38209000	Weak transcription	Brain Substantia Nigra	brain
11	chr19:38190600-38209200	Weak transcription	HSMMtube	muscle
12	chr19:38190800-38209000	Weak transcription	Stomach Mucosa	stomach
13	chr19:38190800-38209200	Weak transcription	Fetal Thymus	thymus
14	chr19:38190800-38209200	Weak transcription	Psoas Muscle	Psoas
15	chr19:38191200-38209200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:38191200-38209200	Weak transcription	Colon Smooth Muscle	Colon
17	chr19:38193800-38209000	Weak transcription	Hela-S3	cervix
18	chr19:38194600-38206600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:38197600-38208800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:38198800-38208800	Weak transcription	Fetal Brain Male	brain
21	chr19:38198800-38209000	Weak transcription	Spleen	Spleen
22	chr19:38198800-38209200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:38198800-38209200	Weak transcription	Gastric	stomach
24	chr19:38198800-38209400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:38198800-38209800	Weak transcription	Esophagus	oesophagus
26	chr19:38199000-38209000	Weak transcription	Fetal Kidney	kidney
27	chr19:38199000-38209000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:38199000-38209200	Weak transcription	Pancreas	Pancrea
29	chr19:38199000-38209200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr19:38199000-38209400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:38199000-38209400	Weak transcription	HSMM	muscle
32	chr19:38199600-38209000	Weak transcription	Small Intestine	intestine
33	chr19:38200400-38209000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:38200400-38209000	Weak transcription	Brain Anterior Caudate	brain
35	chr19:38200400-38209200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr19:38200400-38209200	Weak transcription	NHDF-Ad	bronchial
37	chr19:38200400-38209400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr19:38200600-38209400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:38200800-38206600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:38200800-38208800	Weak transcription	Fetal Brain Female	brain
41	chr19:38200800-38209000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr19:38200800-38209200	Weak transcription	Brain Hippocampus Middle	brain
43	chr19:38200800-38209200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:38201200-38209200	Weak transcription	Thymus	Thymus
45	chr19:38201400-38208800	Weak transcription	Brain Germinal Matrix	brain
46	chr19:38201400-38209200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr19:38202000-38209200	Weak transcription	Colonic Mucosa	Colon
48	chr19:38202400-38209000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr19:38202400-38209200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr19:38202400-38209200	Weak transcription	Osteobl	bone

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