Variant report

Variant	rs9948041
Chromosome Location	chr18:8288568-8288569
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:8286081..8288713-chr18:8292383..8293972,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11876028	0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2012483	0.82[ASN][1000 genomes]
rs2155756	0.81[CHD][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap]
rs59132483	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8086604	0.93[CEU][hapmap]
rs948346	0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv458018	chr18:8110805-8645907	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv576426	chr18:8110805-8645907	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057288	chr18:8218725-8351340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv543639	chr18:8218725-8351340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3351324	chr18:8250514-8405140	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1058445	chr18:8270681-8421249	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	esv275400	chr18:8288568-8290747	Flanking Active TSS Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9948041	RAI14	trans	lymphoblastoid	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8191200-8288600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr18:8245400-8288600	Weak transcription	Aorta	Aorta
3	chr18:8265400-8296600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr18:8270800-8297400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr18:8275200-8296400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr18:8280800-8288600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr18:8281400-8288600	Weak transcription	Fetal Heart	heart
8	chr18:8281400-8288800	Weak transcription	Fetal Brain Male	brain
9	chr18:8281600-8288800	Weak transcription	Spleen	Spleen
10	chr18:8284600-8288800	Weak transcription	Adipose Nuclei	Adipose
11	chr18:8284600-8288800	Weak transcription	Fetal Stomach	stomach
12	chr18:8284600-8298800	Weak transcription	HepG2	liver
13	chr18:8284600-8300600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr18:8284800-8296200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr18:8284800-8296400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr18:8284800-8296600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr18:8284800-8301000	Weak transcription	Osteobl	bone
18	chr18:8285600-8292800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr18:8286200-8289200	Enhancers	Fetal Lung	lung
20	chr18:8286400-8296200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr18:8286400-8298400	Weak transcription	Gastric	stomach
22	chr18:8286600-8291000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr18:8286600-8292000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr18:8286800-8296400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr18:8287000-8289200	Enhancers	Fetal Muscle Leg	muscle
26	chr18:8287200-8289200	Enhancers	Pancreas	Pancrea
27	chr18:8287400-8289000	Enhancers	Psoas Muscle	Psoas
28	chr18:8287400-8289200	Enhancers	Left Ventricle	heart
29	chr18:8287400-8296600	Weak transcription	Thymus	Thymus
30	chr18:8287800-8288800	Weak transcription	Brain Anterior Caudate	brain
31	chr18:8287800-8289200	Enhancers	Lung	lung
32	chr18:8287800-8306800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr18:8288200-8289200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr18:8288200-8289200	Enhancers	Fetal Muscle Trunk	muscle
35	chr18:8288200-8289600	Enhancers	Brain Germinal Matrix	brain
36	chr18:8288200-8292200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr18:8288200-8292600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr18:8288400-8289000	Weak transcription	Fetal Brain Female	brain
39	chr18:8288400-8289200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr18:8288400-8289200	Enhancers	Fetal Kidney	kidney
41	chr18:8288400-8289200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr18:8288400-8290000	Enhancers	Right Atrium	heart
43	chr18:8288400-8297800	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links