Variant report

Variant	rs4088299
Chromosome Location	chr19:38272014-38272015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38083338..38085691-chr19:38270478..38272116,2	K562	blood:

Variant related genes	Relation type
ENSG00000180479	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1056405	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11083434	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11665869	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11666021	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11672440	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12460735	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17249047	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs241935	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs241952	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241954	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241955	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35205379	0.85[AFR][1000 genomes]
rs3848624	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4356596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4510143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60731897	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254809	0.93[EUR][1000 genomes]
rs73025630	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73027418	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73039018	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73041004	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs73041022	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041034	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73041045	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73041047	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8103383	0.94[EUR][1000 genomes];0.85[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	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
4	nsv960835	chr19:38270238-38293706	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38270600-38272200	Weak transcription	Lung	lung
2	chr19:38270800-38272200	Weak transcription	Fetal Intestine Small	intestine
3	chr19:38270800-38272400	Weak transcription	Left Ventricle	heart
4	chr19:38270800-38272400	Weak transcription	Pancreas	Pancrea
5	chr19:38270800-38272800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:38270800-38274400	Weak transcription	Psoas Muscle	Psoas
7	chr19:38270800-38276400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:38270800-38277600	Weak transcription	Ovary	ovary
9	chr19:38270800-38277800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:38270800-38279800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:38270800-38281000	Weak transcription	Right Ventricle	heart
12	chr19:38270800-38281400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:38271000-38273400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:38271000-38275200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:38271000-38281000	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:38271200-38272400	Weak transcription	Adipose Nuclei	Adipose
17	chr19:38271200-38272800	Weak transcription	Primary T cells from cord blood	blood
18	chr19:38271200-38274600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:38271400-38272200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:38271400-38272200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:38271400-38272600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:38271400-38275400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:38271400-38276600	Weak transcription	Fetal Lung	lung
24	chr19:38271400-38281000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr19:38271600-38272200	Weak transcription	Liver	Liver
26	chr19:38272000-38274200	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links