Variant report

Variant	rs57962499
Chromosome Location	chr19:18845785-18845786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12984991	0.99[ASN][1000 genomes]
rs17757406	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2075017	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240887	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808154	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4808851	0.97[ASN][1000 genomes]
rs4808852	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808853	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56182405	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56210931	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58406187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61447117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510997	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6510998	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6510999	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511000	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511001	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71332136	0.96[ASN][1000 genomes]
rs71332137	0.99[ASN][1000 genomes]
rs71332138	0.99[ASN][1000 genomes]
rs7251560	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251710	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252217	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256502	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258259	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73537985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73537994	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73537995	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18820400-18847200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr19:18820600-18846600	Weak transcription	Esophagus	oesophagus
3	chr19:18821200-18860600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr19:18821200-18861000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr19:18821200-18864800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr19:18824200-18846600	Weak transcription	Pancreas	Pancrea
7	chr19:18824600-18847800	Weak transcription	Liver	Liver
8	chr19:18827000-18846200	Weak transcription	Thymus	Thymus
9	chr19:18827600-18860600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:18828800-18850400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:18829200-18860000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr19:18829200-18861400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr19:18830400-18845800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:18830800-18845800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr19:18833800-18853400	Weak transcription	Primary T cells from cord blood	blood
16	chr19:18833800-18860400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr19:18833800-18860800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:18834600-18845800	Weak transcription	Brain Anterior Caudate	brain
19	chr19:18835000-18860600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr19:18835200-18853200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:18841200-18852000	Weak transcription	Small Intestine	intestine
22	chr19:18841600-18845800	Weak transcription	Spleen	Spleen
23	chr19:18842000-18848400	Enhancers	Fetal Muscle Leg	muscle
24	chr19:18842200-18853400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:18842600-18845800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:18842600-18851000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr19:18842600-18853400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr19:18842800-18846400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:18842800-18856600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:18842800-18861000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr19:18843000-18860600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:18843600-18845800	Enhancers	Fetal Stomach	stomach
33	chr19:18843800-18846800	Enhancers	Brain Germinal Matrix	brain
34	chr19:18843800-18848400	Enhancers	Placenta	Placenta
35	chr19:18844200-18845800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:18844200-18872800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:18844400-18845800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:18844400-18845800	Weak transcription	Brain Substantia Nigra	brain
39	chr19:18844400-18845800	Weak transcription	Fetal Brain Male	brain
40	chr19:18844400-18847400	Weak transcription	Colonic Mucosa	Colon
41	chr19:18844400-18848200	Enhancers	Fetal Heart	heart
42	chr19:18844400-18848600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr19:18844400-18859800	Weak transcription	Fetal Brain Female	brain
44	chr19:18844400-18867400	Weak transcription	HSMMtube	muscle
45	chr19:18844600-18846000	Weak transcription	HSMM	muscle
46	chr19:18844600-18846400	Weak transcription	Gastric	stomach
47	chr19:18844600-18846400	Weak transcription	Right Ventricle	heart
48	chr19:18844600-18846800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr19:18844600-18847800	Weak transcription	Lung	lung
50	chr19:18844600-18847800	Enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links