Variant report

Variant	rs13258902
Chromosome Location	chr8:130365025-130365026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GSDMC-1	chr8:130363938-130365226	XLOC_007221
2	lnc-GSDMC-1	chr8:130364675-130365226	ENSG00000229140
3	lnc-GSDMC-1	chr8:130363937-130365226	ENSG00000229140
4	lnc-GSDMC-1	chr8:130363937-130365226	ENSG00000229140
5	lnc-GSDMC-1	chr8:130363940-130365228	NONHSAT129116
6	lnc-GSDMC-1	chr8:130364905-130365234	ENSG00000229140.4

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10505535	0.85[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10505536	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12056871	0.84[ASN][1000 genomes]
rs13280005	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1835849	0.82[ASN][1000 genomes]
rs1835850	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2099290	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2099291	0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2099292	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2436206	0.82[ASN][1000 genomes]
rs2568441	0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2568442	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2568444	0.82[ASN][1000 genomes]
rs2568446	0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2568448	0.95[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2568449	0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2568451	0.81[ASN][1000 genomes]
rs2568452	0.80[ASN][1000 genomes]
rs2579854	0.82[ASN][1000 genomes]
rs2579855	0.91[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2579859	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2719190	0.85[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs2719192	0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2719193	0.91[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4733546	0.82[ASN][1000 genomes]
rs7003796	0.84[ASN][1000 genomes]
rs7004036	0.84[ASN][1000 genomes]
rs891837	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831460	chr8:130185680-130366217	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:130355000-130368400	Strong transcription	K562	blood
2	chr8:130361600-130368400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr8:130361600-130370800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr8:130361800-130371000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr8:130364400-130365800	Genic enhancers	Dnd41	blood
6	chr8:130364600-130365400	Enhancers	Thymus	Thymus
7	chr8:130364600-130365800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:130364600-130365800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr8:130364800-130365400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr8:130364800-130365400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr8:130364800-130365800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr8:130364800-130365800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr8:130364800-130365800	Enhancers	HMEC	breast
14	chr8:130364800-130365800	Enhancers	HSMM	muscle
15	chr8:130364800-130366000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr8:130365000-130365200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr8:130365000-130365200	Active TSS	HSMMtube	muscle
18	chr8:130365000-130365400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr8:130365000-130365400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr8:130365000-130365400	Flanking Active TSS	NHEK	skin
21	chr8:130365000-130365600	Enhancers	Ovary	ovary
22	chr8:130365000-130365800	Enhancers	Fetal Thymus	thymus

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