Variant report

Variant	rs2411312
Chromosome Location	chr15:39944693-39944694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1004739	0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1004740	0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1004741	0.84[EUR][1000 genomes]
rs11633974	0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs11638500	0.92[EUR][1000 genomes]
rs11856294	0.84[EUR][1000 genomes]
rs11857927	0.82[EUR][1000 genomes]
rs12901142	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12903514	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12911549	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs16969445	0.84[EUR][1000 genomes]
rs16969460	0.84[EUR][1000 genomes]
rs2129458	0.82[EUR][1000 genomes]
rs2411299	1.00[CEU][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs2411301	0.80[MEX][hapmap]
rs2411307	0.80[MEX][hapmap]
rs2411308	0.82[AMR][1000 genomes]
rs2411309	0.90[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2411311	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2412409	0.84[EUR][1000 genomes]
rs2412410	0.84[EUR][1000 genomes]
rs2412411	0.84[EUR][1000 genomes]
rs2412424	0.82[EUR][1000 genomes]
rs2631700	0.91[MEX][hapmap]
rs2631708	0.82[EUR][1000 genomes]
rs2631709	0.82[EUR][1000 genomes]
rs2631712	0.82[EUR][1000 genomes]
rs2664124	0.82[EUR][1000 genomes]
rs28437905	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2898685	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs34275067	0.92[EUR][1000 genomes]
rs35754803	0.83[EUR][1000 genomes]
rs3784390	0.81[TSI][hapmap]
rs4476147	0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs4480779	0.84[AMR][1000 genomes]
rs4526992	0.95[AFR][1000 genomes]
rs4606692	1.00[CEU][hapmap]
rs56722485	0.84[EUR][1000 genomes]
rs57969006	0.84[EUR][1000 genomes]
rs58332880	0.83[EUR][1000 genomes]
rs60884629	0.81[EUR][1000 genomes]
rs6492909	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7167100	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7167184	1.00[CEU][hapmap]
rs8033902	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8034885	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8035895	0.82[EUR][1000 genomes]
rs8036226	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8042068	0.82[AMR][1000 genomes]
rs937960	0.80[MEX][hapmap]
rs9672572	0.81[AMR][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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2411312	THBS1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39938000-39950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:39938000-39957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:39938200-39950800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:39944200-39944800	Enhancers	Fetal Lung	lung
5	chr15:39944400-39945000	Enhancers	HSMMtube	muscle
6	chr15:39944600-39947400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links