Variant report

Variant	rs12235233
Chromosome Location	chr9:86041629-86041630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10116367	0.94[ASN][1000 genomes]
rs10868005	0.81[JPT][hapmap]
rs10868006	0.81[JPT][hapmap]
rs10868008	0.81[YRI][hapmap];0.92[AFR][1000 genomes]
rs11140069	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs11140077	0.81[YRI][hapmap];0.92[AFR][1000 genomes]
rs11140078	0.81[JPT][hapmap]
rs11140079	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140082	0.81[JPT][hapmap]
rs11140083	0.81[JPT][hapmap]
rs11140086	0.83[YRI][hapmap];0.92[AFR][1000 genomes]
rs11140092	0.81[YRI][hapmap];0.92[AFR][1000 genomes]
rs12683112	0.92[AFR][1000 genomes]
rs12685254	0.82[AFR][1000 genomes]
rs17086237	0.85[AFR][1000 genomes]
rs17086255	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3860918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4537377	0.81[JPT][hapmap]
rs4636280	0.81[JPT][hapmap]
rs56009714	0.83[AFR][1000 genomes]
rs56039713	0.98[AFR][1000 genomes]
rs72745064	0.92[AFR][1000 genomes]
rs72745071	0.92[AFR][1000 genomes]
rs7856827	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875766	0.92[AFR][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	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1048086	chr9:86040900-86059732	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86037800-86047200	Weak transcription	Fetal Stomach	stomach
2	chr9:86038400-86045800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:86038400-86046600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:86039200-86050000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:86040000-86045800	Weak transcription	Fetal Lung	lung
6	chr9:86040000-86045800	Weak transcription	Small Intestine	intestine
7	chr9:86040000-86046000	Weak transcription	Fetal Heart	heart
8	chr9:86040200-86046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:86040400-86045800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:86040400-86050000	Weak transcription	Fetal Intestine Large	intestine
11	chr9:86040800-86042400	Enhancers	Left Ventricle	heart
12	chr9:86041000-86041800	Enhancers	Ovary	ovary
13	chr9:86041000-86041800	Enhancers	Spleen	Spleen
14	chr9:86041000-86042200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr9:86041000-86042200	Enhancers	Aorta	Aorta
16	chr9:86041000-86042400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:86041000-86042400	Enhancers	Adipose Nuclei	Adipose
18	chr9:86041000-86042400	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr9:86041200-86041800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:86041200-86042000	Enhancers	Fetal Muscle Leg	muscle
21	chr9:86041200-86042000	Genic enhancers	HepG2	liver
22	chr9:86041200-86042200	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr9:86041200-86042200	Enhancers	Colon Smooth Muscle	Colon
24	chr9:86041200-86042200	Enhancers	Lung	lung
25	chr9:86041200-86042200	Enhancers	Right Atrium	heart
26	chr9:86041200-86042200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr9:86041200-86042400	Enhancers	Gastric	stomach
28	chr9:86041400-86041800	Enhancers	Brain Angular Gyrus	brain
29	chr9:86041400-86041800	Enhancers	Pancreas	Pancrea
30	chr9:86041400-86041800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr9:86041400-86041800	Enhancers	Stomach Smooth Muscle	stomach
32	chr9:86041400-86042200	Enhancers	Brain Cingulate Gyrus	brain
33	chr9:86041400-86042200	Enhancers	Psoas Muscle	Psoas
34	chr9:86041400-86042200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr9:86041600-86041800	Enhancers	Duodenum Mucosa	Duodenum
36	chr9:86041600-86042400	Enhancers	Right Ventricle	heart
37	chr9:86041600-86045800	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links