Variant report

Variant	rs9964644
Chromosome Location	chr18:8178318-8178319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10513900	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs11081363	0.85[EUR][1000 genomes]
rs11663439	0.98[ASN][1000 genomes]
rs11664606	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11665298	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11874230	0.92[ASN][1000 genomes]
rs12954922	0.98[ASN][1000 genomes]
rs12962187	0.83[EUR][1000 genomes]
rs12963432	0.82[CHB][hapmap]
rs2098264	0.94[CHB][hapmap];0.86[CHD][hapmap];0.88[ASN][1000 genomes]
rs2192194	0.97[ASN][1000 genomes]
rs2286934	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[ASN][1000 genomes]
rs2302502	0.82[CHD][hapmap]
rs7232316	0.85[EUR][1000 genomes]
rs7233623	0.82[EUR][1000 genomes]
rs7244386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs759095	0.91[EUR][1000 genomes]
rs8087582	0.91[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
rs9964644	PTPRM	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8170800-8225400	Weak transcription	Aorta	Aorta
2	chr18:8174000-8179200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr18:8174800-8178600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr18:8175000-8178400	Enhancers	Fetal Kidney	kidney
5	chr18:8175000-8195000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:8175600-8178400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr18:8175800-8178400	Enhancers	Hela-S3	cervix
8	chr18:8175800-8178400	Enhancers	HepG2	liver
9	chr18:8176800-8178600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr18:8177000-8178600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr18:8177000-8180600	Weak transcription	NHDF-Ad	bronchial
12	chr18:8177400-8180600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr18:8177600-8182800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr18:8177600-8187600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr18:8177800-8192800	Weak transcription	Fetal Heart	heart
16	chr18:8178000-8178400	Weak transcription	Lung	lung
17	chr18:8178000-8185400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr18:8178000-8186600	Weak transcription	Left Ventricle	heart
19	chr18:8178000-8186600	Weak transcription	Pancreas	Pancrea
20	chr18:8178000-8190800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr18:8178000-8191200	Weak transcription	Gastric	stomach
22	chr18:8178000-8192400	Weak transcription	A549	lung
23	chr18:8178000-8193600	Weak transcription	Ovary	ovary
24	chr18:8178000-8198400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr18:8178000-8204800	Weak transcription	Right Ventricle	heart
26	chr18:8178000-8230000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr18:8178200-8186600	Weak transcription	Colon Smooth Muscle	Colon
28	chr18:8178200-8191000	Weak transcription	Psoas Muscle	Psoas
29	chr18:8178200-8200200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr18:8178200-8212400	Weak transcription	Adipose Nuclei	Adipose
31	chr18:8178200-8216400	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links