Variant report

Variant	rs56293547
Chromosome Location	chr19:38574772-38574773
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10405667	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1568975	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1614979	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1622409	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1625884	0.87[EUR][1000 genomes]
rs1654355	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1654357	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1654358	0.89[EUR][1000 genomes]
rs1654359	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1654365	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1654367	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725461	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1725473	0.86[EUR][1000 genomes]
rs1725479	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725512	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28581256	0.83[EUR][1000 genomes]
rs3760882	0.87[EUR][1000 genomes]
rs3810356	0.87[EUR][1000 genomes]
rs4802233	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802239	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802247	0.83[EUR][1000 genomes]
rs4803786	0.82[EUR][1000 genomes]
rs4803800	0.80[AMR][1000 genomes]
rs4803802	0.80[AMR][1000 genomes]
rs56166457	0.86[EUR][1000 genomes]
rs58152231	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59185302	0.82[EUR][1000 genomes]
rs59579475	0.86[EUR][1000 genomes]
rs59924887	0.82[EUR][1000 genomes]
rs61388128	0.82[EUR][1000 genomes]
rs705505	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs729625	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729626	0.89[EUR][1000 genomes]
rs735615	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105468	0.82[EUR][1000 genomes]
rs8106266	0.80[AMR][1000 genomes]
rs855598	0.83[ASN][1000 genomes]
rs855599	0.81[ASN][1000 genomes]
rs855619	0.89[EUR][1000 genomes]
rs855621	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs855623	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs855624	0.89[EUR][1000 genomes]
rs855625	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs855627	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs855630	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs855631	0.82[AMR][1000 genomes]
rs855633	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs855634	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs855638	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs855640	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs855641	0.87[EUR][1000 genomes]
rs860623	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs863020	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs941039	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs941040	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9941467	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
2	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:38554800-38580200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr19:38564800-38579000	Weak transcription	Fetal Lung	lung
6	chr19:38565000-38579200	Weak transcription	Brain Substantia Nigra	brain
7	chr19:38565600-38588400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:38567600-38605400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:38568000-38590200	Strong transcription	Fetal Intestine Small	intestine
10	chr19:38570600-38579000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr19:38570800-38584000	Weak transcription	Right Atrium	heart
12	chr19:38570800-38590200	Weak transcription	Fetal Thymus	thymus
13	chr19:38571000-38580800	Weak transcription	Hela-S3	cervix
14	chr19:38571000-38590000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:38571000-38590200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:38571200-38578800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:38571200-38579400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:38571200-38580000	Weak transcription	HSMMtube	muscle
19	chr19:38571200-38580200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:38571200-38590200	Weak transcription	HMEC	breast
21	chr19:38571200-38590200	Weak transcription	NHEK	skin
22	chr19:38571400-38579200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:38571400-38579200	Weak transcription	HepG2	liver
24	chr19:38571400-38586000	Strong transcription	A549	lung
25	chr19:38571600-38575200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:38571600-38579200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:38571800-38575000	Strong transcription	Primary T cells from cord blood	blood
28	chr19:38571800-38575000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:38571800-38575000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr19:38571800-38575000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr19:38571800-38575800	Strong transcription	Primary B cells from cord blood	blood
32	chr19:38571800-38582600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:38571800-38585000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:38571800-38585400	Strong transcription	Fetal Stomach	stomach
35	chr19:38571800-38586000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:38571800-38586600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:38572000-38574800	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr19:38572000-38574800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr19:38572000-38575000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:38572000-38575000	Strong transcription	Osteobl	bone
41	chr19:38572000-38575200	Strong transcription	Fetal Muscle Leg	muscle
42	chr19:38572000-38575400	Strong transcription	GM12878-XiMat	blood
43	chr19:38572000-38585800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr19:38572000-38586000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:38572200-38576200	Weak transcription	HSMM	muscle
46	chr19:38572200-38579000	Weak transcription	NH-A	brain
47	chr19:38572200-38585800	Weak transcription	NHDF-Ad	bronchial
48	chr19:38572400-38576000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:38572400-38579400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:38572400-38581400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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