Variant report

Variant	rs1537720
Chromosome Location	chr9:117897543-117897544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10125663	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10817713	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982553	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1335332	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1335333	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1414137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537015	0.82[ASW][hapmap];0.83[CEU][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1537016	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071520	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4978621	0.80[ASW][hapmap];0.82[GIH][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap]
rs4979496	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4979505	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs60632414	0.93[AFR][1000 genomes]
rs6478134	0.82[AFR][1000 genomes]
rs7033521	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs7034038	0.86[ASW][hapmap];0.82[GIH][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs7853883	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs884290	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs945256	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs945257	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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	4 gene(s)	inside rSNPs	diseases
5	nsv6681	chr9:117893926-117938609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1537720	TNC	cis	lymphoblastoid	seeQTL
rs1537720	TNC	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117890200-117909000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:117894200-117898800	Enhancers	Fetal Stomach	stomach
3	chr9:117894800-117899200	Enhancers	NHDF-Ad	bronchial
4	chr9:117895200-117898200	Weak transcription	Esophagus	oesophagus
5	chr9:117895200-117898800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:117895200-117899400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:117895400-117897600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:117895400-117897600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:117895400-117897800	Enhancers	Osteobl	bone
10	chr9:117895400-117900000	Enhancers	NHLF	lung
11	chr9:117895400-117903200	Weak transcription	Fetal Kidney	kidney
12	chr9:117896200-117899200	Enhancers	Rectal Smooth Muscle	rectum
13	chr9:117896200-117899800	Enhancers	Colon Smooth Muscle	Colon
14	chr9:117896600-117900400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:117896800-117899000	Enhancers	Stomach Smooth Muscle	stomach
16	chr9:117896800-117900200	Enhancers	Fetal Lung	lung
17	chr9:117897200-117897600	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:117897200-117898200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:117897400-117898200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links