Variant report

Variant	rs12960691
Chromosome Location	chr18:11668861-11668862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-677O4.1.1-1	chr18:11666455-11670156	NONHSAT058101

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12454527	0.83[ASN][1000 genomes]
rs12605129	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12607424	0.93[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs12607713	0.83[ASN][1000 genomes]
rs12954257	0.91[ASN][1000 genomes]
rs12957891	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs12961855	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12962122	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12962341	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12964976	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12966339	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12966486	0.91[ASN][1000 genomes]
rs12967201	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12967203	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12971196	0.80[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs35150497	0.88[ASN][1000 genomes]
rs4541146	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56392464	0.86[ASN][1000 genomes]
rs7226488	0.88[ASN][1000 genomes]
rs7230653	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231146	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066659	chr18:11246502-11709409	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12960691	LASP1	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11666400-11669400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr18:11667200-11669200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr18:11668400-11669400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr18:11668400-11669400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr18:11668400-11669400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr18:11668400-11669400	Enhancers	HMEC	breast
7	chr18:11668400-11669600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:11668600-11669200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr18:11668600-11669400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr18:11668600-11669400	Enhancers	NHEK	skin
11	chr18:11668600-11669600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr18:11668800-11669000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr18:11668800-11669200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr18:11668800-11669600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr18:11668800-11670400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr18:11668800-11670400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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