Variant report

Variant	rs2518713
Chromosome Location	chr9:21929666-21929667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf53-5	chr9:21929456-21931072	NONHSAT130405

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10811638	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10965183	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10965186	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2188125	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2518712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2518714	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2518715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2811715	1.00[CEU][hapmap];0.95[CHD][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4977570	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4977746	0.89[CEU][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs4977747	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977748	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4977749	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6475597	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7852128	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7852234	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7864029	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7869004	0.89[CEU][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2518713	MTAP	cis	parietal	SCAN
rs2518713	MTAP	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21905400-21931000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:21911000-21931200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:21911000-21935800	Weak transcription	HSMM	muscle
4	chr9:21916600-21930800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:21919800-21931000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:21919800-21931000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:21919800-21932800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:21920000-21931200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:21920200-21930400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:21920200-21931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:21920400-21931400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr9:21920400-21931600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:21920600-21935000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:21920600-21942600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:21920800-21932000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:21921200-21931000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:21921200-21934000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:21921200-21935600	Weak transcription	Primary T cells from cord blood	blood
19	chr9:21922200-21932400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:21922200-21933000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:21922800-21931000	Weak transcription	Aorta	Aorta
22	chr9:21923200-21930000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:21923600-21931000	Weak transcription	Fetal Stomach	stomach
24	chr9:21923800-21934000	Weak transcription	Thymus	Thymus
25	chr9:21923800-21934800	Weak transcription	Dnd41	blood
26	chr9:21924000-21934600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr9:21924800-21933000	Weak transcription	Lung	lung
28	chr9:21926200-21931200	Weak transcription	NHEK	skin
29	chr9:21927000-21933400	Weak transcription	HSMMtube	muscle
30	chr9:21928000-21934800	Weak transcription	Psoas Muscle	Psoas
31	chr9:21928600-21931000	Weak transcription	Left Ventricle	heart
32	chr9:21928600-21931200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:21928600-21931200	Weak transcription	Osteobl	bone
34	chr9:21928600-21931800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:21928600-21933200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:21928800-21930400	Weak transcription	Right Ventricle	heart
37	chr9:21928800-21933000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:21929000-21930800	Weak transcription	Ovary	ovary
39	chr9:21929200-21931000	Weak transcription	Adipose Nuclei	Adipose
40	chr9:21929200-21931000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr9:21929200-21932600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr9:21929400-21931000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:21929600-21931200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr9:21929600-21932800	Weak transcription	Gastric	stomach
45	chr9:21929600-21933800	Weak transcription	Liver	Liver

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