Variant report

Variant	rs4296399
Chromosome Location	chr2:173891021-173891022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12612593	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12614386	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12615974	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12618296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034647	1.00[AFR][1000 genomes]
rs16861180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34252442	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35730673	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3769218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs3769221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3769223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41268707	1.00[AFR][1000 genomes]
rs6735942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7585995	1.00[AFR][1000 genomes];0.97[ASN][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	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173856200-173892600	Weak transcription	Brain Angular Gyrus	brain
2	chr2:173868000-173902000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:173868600-173892200	Weak transcription	Fetal Intestine Large	intestine
4	chr2:173877200-173901600	Weak transcription	Gastric	stomach
5	chr2:173880800-173891600	Strong transcription	Liver	Liver
6	chr2:173881200-173892400	Weak transcription	Fetal Intestine Small	intestine
7	chr2:173881200-173912800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:173881400-173897200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:173883000-173892200	Weak transcription	Right Atrium	heart
10	chr2:173884800-173893000	Weak transcription	Right Ventricle	heart
11	chr2:173885400-173892000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:173885400-173892600	Weak transcription	Brain Anterior Caudate	brain
13	chr2:173887000-173891400	Weak transcription	Fetal Lung	lung
14	chr2:173887200-173891800	Weak transcription	A549	lung
15	chr2:173887200-173892200	Weak transcription	Adipose Nuclei	Adipose
16	chr2:173887200-173892400	Weak transcription	Hela-S3	cervix
17	chr2:173887200-173892600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:173887200-173893000	Weak transcription	Psoas Muscle	Psoas
19	chr2:173887400-173891400	Weak transcription	Fetal Heart	heart
20	chr2:173887400-173892000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:173887400-173894800	Weak transcription	Left Ventricle	heart
22	chr2:173888000-173892600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:173888400-173892000	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:173888600-173892200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:173888600-173892600	Weak transcription	Ovary	ovary
26	chr2:173888800-173892000	Weak transcription	Fetal Stomach	stomach
27	chr2:173888800-173905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:173888800-173906600	Weak transcription	Lung	lung
29	chr2:173890000-173892000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:173890000-173892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:173890600-173891600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr2:173890600-173892000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:173890600-173894000	Enhancers	NHDF-Ad	bronchial
34	chr2:173890800-173891200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:173890800-173891400	Enhancers	Fetal Muscle Leg	muscle
36	chr2:173891000-173892200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:173891000-173896200	Weak transcription	Placenta	Placenta
38	chr2:173891000-173908000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links