Variant report

Variant	rs2286934
Chromosome Location	chr18:8175530-8175531
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	chr18:8175161..8177762-chr3:171759970..171761579,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10513900	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106701	0.90[CEU][hapmap];0.84[GIH][hapmap];0.85[AMR][1000 genomes]
rs11663439	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11664606	0.88[ASN][1000 genomes]
rs11665298	0.92[ASN][1000 genomes]
rs11874230	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12953658	0.80[ASN][1000 genomes]
rs12954922	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12962187	0.83[ASN][1000 genomes]
rs12963432	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs2098264	0.86[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2192194	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6506557	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7241083	0.90[CEU][hapmap]
rs7244386	0.98[ASN][1000 genomes]
rs8087582	0.95[ASN][1000 genomes]
rs9964644	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv458020	chr18:8161470-8183260	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv576427	chr18:8161470-8183260	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv909360	chr18:8167050-8207445	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2286934	PTPRM	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8159000-8176600	Weak transcription	Pancreas	Pancrea
2	chr18:8159000-8177400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr18:8161600-8176600	Weak transcription	Spleen	Spleen
4	chr18:8163000-8177400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr18:8163200-8177800	Weak transcription	Lung	lung
6	chr18:8163600-8175600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr18:8168000-8177400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:8170200-8175800	Weak transcription	Fetal Brain Male	brain
9	chr18:8170800-8225400	Weak transcription	Aorta	Aorta
10	chr18:8173200-8175800	Weak transcription	A549	lung
11	chr18:8173800-8177600	Enhancers	Brain Germinal Matrix	brain
12	chr18:8174000-8176200	Enhancers	Fetal Brain Female	brain
13	chr18:8174000-8179200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr18:8174400-8177800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr18:8174400-8178200	Enhancers	Colon Smooth Muscle	Colon
16	chr18:8174600-8176000	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr18:8174600-8176000	Enhancers	Psoas Muscle	Psoas
18	chr18:8174600-8178200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr18:8174800-8176000	Enhancers	Left Ventricle	heart
20	chr18:8174800-8177200	Enhancers	Brain Angular Gyrus	brain
21	chr18:8174800-8177800	Enhancers	Fetal Heart	heart
22	chr18:8174800-8177800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr18:8174800-8178000	Enhancers	Brain Cingulate Gyrus	brain
24	chr18:8174800-8178000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr18:8174800-8178000	Enhancers	Stomach Smooth Muscle	stomach
26	chr18:8174800-8178200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr18:8174800-8178200	Enhancers	Brain Hippocampus Middle	brain
28	chr18:8174800-8178200	Enhancers	Rectal Smooth Muscle	rectum
29	chr18:8174800-8178200	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr18:8174800-8178600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr18:8175000-8175600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr18:8175000-8175600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr18:8175000-8176000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr18:8175000-8176200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr18:8175000-8176800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr18:8175000-8178400	Enhancers	Fetal Kidney	kidney
37	chr18:8175000-8195000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr18:8175200-8176200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr18:8175200-8176400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr18:8175200-8176400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr18:8175200-8176600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr18:8175200-8176800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr18:8175400-8177000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr18:8175400-8178000	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links