Variant report

Variant	rs55905728
Chromosome Location	chr3:160530360-160530361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1455870	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1455871	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831442	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16831457	0.94[EUR][1000 genomes]
rs16831471	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16831473	1.00[EUR][1000 genomes]
rs16831516	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831520	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236620	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17236641	0.91[EUR][1000 genomes]
rs17236648	1.00[EUR][1000 genomes]
rs17236655	1.00[EUR][1000 genomes]
rs17236662	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17826352	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17826358	0.94[EUR][1000 genomes]
rs17826364	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17826370	1.00[EUR][1000 genomes]
rs17826376	1.00[EUR][1000 genomes]
rs2068817	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34035435	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3907061	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549318	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627794	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55891037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923270	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55997050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56083575	1.00[EUR][1000 genomes]
rs56141155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157815	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56180903	1.00[EUR][1000 genomes]
rs56331465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57828617	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58891820	1.00[EUR][1000 genomes]
rs6771910	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779461	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73877952	1.00[EUR][1000 genomes]
rs73877966	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7618082	1.00[EUR][1000 genomes]
rs7618596	1.00[EUR][1000 genomes]
rs7629154	1.00[EUR][1000 genomes]
rs7633401	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160523000-160532800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:160525800-160530400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:160525800-160530600	Enhancers	Fetal Brain Female	brain
4	chr3:160525800-160530800	Enhancers	Fetal Brain Male	brain
5	chr3:160526000-160530600	Enhancers	Colon Smooth Muscle	Colon
6	chr3:160526400-160530600	Enhancers	Brain Anterior Caudate	brain
7	chr3:160526600-160530400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:160526600-160530400	Weak transcription	Fetal Heart	heart
9	chr3:160527400-160530600	Enhancers	Stomach Smooth Muscle	stomach
10	chr3:160527800-160530600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:160528200-160537600	Weak transcription	Hela-S3	cervix
12	chr3:160528400-160533000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:160528600-160530400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:160528600-160530800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:160529000-160530600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:160529000-160534400	Weak transcription	Aorta	Aorta
17	chr3:160529200-160530600	Enhancers	Fetal Muscle Leg	muscle
18	chr3:160529200-160533800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:160529600-160530600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:160529600-160530600	Enhancers	Left Ventricle	heart
21	chr3:160529600-160530800	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr3:160529600-160530800	Enhancers	Psoas Muscle	Psoas
23	chr3:160529800-160530600	Enhancers	Brain Hippocampus Middle	brain
24	chr3:160529800-160530600	Enhancers	Gastric	stomach
25	chr3:160529800-160533000	Weak transcription	Brain Substantia Nigra	brain
26	chr3:160530200-160530600	Flanking Active TSS	Brain Angular Gyrus	brain
27	chr3:160530200-160530600	Enhancers	Brain Germinal Matrix	brain
28	chr3:160530200-160530600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr3:160530200-160530600	Enhancers	Colonic Mucosa	Colon
30	chr3:160530200-160530600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links