Variant report

Variant	rs56206115
Chromosome Location	chr19:36686205-36686206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10403738	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10407835	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10407850	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10409983	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10412832	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10415410	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10416509	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10416742	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10416925	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10419269	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10425166	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11882933	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12459704	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460466	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12461077	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12461112	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12461855	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28414272	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28528757	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4361039	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4806284	0.90[EUR][1000 genomes]
rs4806293	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4806294	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4806295	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56316708	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56686317	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57385903	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57734651	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59026641	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59295196	0.87[ASN][1000 genomes]
rs61413061	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62113093	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62113146	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251745	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73038028	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73040107	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8106135	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8111860	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56206115	LINC00665	cis	Muscle Skeletal	GTEx
rs56206115	LINC00665	cis	Nerve Tibial	GTEx
rs56206115	ZNF545	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36661800-36686800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:36669600-36704800	Weak transcription	Psoas Muscle	Psoas
3	chr19:36673800-36704800	Weak transcription	Fetal Kidney	kidney
4	chr19:36674000-36704800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:36674200-36687200	Weak transcription	GM12878-XiMat	blood
6	chr19:36674400-36690000	Weak transcription	NHDF-Ad	bronchial
7	chr19:36674400-36704600	Weak transcription	Fetal Brain Male	brain
8	chr19:36674600-36687200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:36674600-36687200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:36674600-36687400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:36674600-36687800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:36674600-36704600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:36674600-36704600	Weak transcription	HMEC	breast
14	chr19:36674600-36704600	Weak transcription	NH-A	brain
15	chr19:36674600-36704600	Weak transcription	NHEK	skin
16	chr19:36674600-36704800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr19:36674800-36694400	Weak transcription	Fetal Heart	heart
18	chr19:36682600-36687200	Weak transcription	Hela-S3	cervix
19	chr19:36682600-36705000	Weak transcription	Small Intestine	intestine
20	chr19:36682800-36687800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:36684600-36686400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:36684600-36686400	Strong transcription	HSMMtube	muscle
23	chr19:36684600-36686800	Strong transcription	Brain Germinal Matrix	brain
24	chr19:36684800-36686400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr19:36685000-36686400	Strong transcription	Fetal Lung	lung
26	chr19:36685200-36704800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:36685400-36687600	Weak transcription	Fetal Thymus	thymus
28	chr19:36685400-36704600	Weak transcription	HSMM	muscle
29	chr19:36685800-36687200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr19:36685800-36687600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr19:36685800-36687600	Weak transcription	Stomach Mucosa	stomach
32	chr19:36685800-36699400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:36685800-36704600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr19:36685800-36704800	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:36686000-36687200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:36686000-36687200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr19:36686000-36687400	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:36686000-36687800	Weak transcription	Brain Substantia Nigra	brain
39	chr19:36686000-36687800	Weak transcription	HepG2	liver
40	chr19:36686000-36688000	Weak transcription	NHLF	lung
41	chr19:36686000-36688400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr19:36686000-36688600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr19:36686000-36688800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:36686000-36689800	Weak transcription	Primary T cells from cord blood	blood
45	chr19:36686000-36690400	Weak transcription	Fetal Intestine Small	intestine
46	chr19:36686000-36691600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:36686000-36692000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:36686000-36692000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:36686000-36692000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:36686000-36692000	Weak transcription	Right Ventricle	heart

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