Variant report

Variant	rs55683539
Chromosome Location	chr9:21542134-21542135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10491567	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10811549	0.89[EUR][1000 genomes]
rs10811551	0.87[EUR][1000 genomes]
rs10811556	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10811557	0.81[AMR][1000 genomes]
rs10811562	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10811563	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811564	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10811565	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10811566	0.90[ASN][1000 genomes]
rs10811568	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10965019	0.82[EUR][1000 genomes]
rs10965024	0.82[EUR][1000 genomes]
rs10965031	0.87[EUR][1000 genomes]
rs10965034	0.82[EUR][1000 genomes]
rs10965036	0.82[EUR][1000 genomes]
rs10965049	0.95[ASN][1000 genomes]
rs10965050	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10965053	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10965054	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10965059	0.95[EUR][1000 genomes]
rs10965060	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10965063	0.89[EUR][1000 genomes]
rs1125488	0.84[EUR][1000 genomes]
rs12375583	0.82[EUR][1000 genomes]
rs12377379	0.95[EUR][1000 genomes]
rs12378286	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12378990	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12379382	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12379709	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12379721	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1332188	0.82[EUR][1000 genomes]
rs16938433	0.82[EUR][1000 genomes]
rs16938435	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16938448	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2039380	0.85[EUR][1000 genomes]
rs55835613	0.95[EUR][1000 genomes]
rs56122777	0.95[EUR][1000 genomes]
rs56337511	0.82[EUR][1000 genomes]
rs7026731	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7032680	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7041183	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72703410	0.80[EUR][1000 genomes]
rs72703411	0.87[EUR][1000 genomes]
rs72703417	0.82[EUR][1000 genomes]
rs72703418	0.82[EUR][1000 genomes]
rs72703419	0.82[EUR][1000 genomes]
rs72703426	0.82[EUR][1000 genomes]
rs72703442	0.82[AMR][1000 genomes]
rs72703445	0.95[EUR][1000 genomes]
rs72703447	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72703448	0.96[ASN][1000 genomes]
rs72703449	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72703450	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9644855	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892740	chr9:21471499-21551513	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases
2	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
4	nsv892741	chr9:21517302-21551513	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21507200-21551400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:21516800-21542600	Weak transcription	Stomach Mucosa	stomach
3	chr9:21529000-21551400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:21531600-21542600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr9:21532200-21542800	Weak transcription	NHLF	lung
6	chr9:21533200-21542600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:21534000-21543000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:21534000-21544200	Weak transcription	NHDF-Ad	bronchial
9	chr9:21534400-21548200	Weak transcription	HSMM	muscle
10	chr9:21536000-21543000	Weak transcription	NH-A	brain
11	chr9:21536200-21542200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:21536400-21544400	Weak transcription	Hela-S3	cervix
13	chr9:21536400-21546800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:21536400-21552200	Weak transcription	Gastric	stomach
15	chr9:21536600-21542600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:21536600-21548400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:21536600-21549600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:21536800-21542800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:21542000-21542200	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:21542000-21542200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:21542000-21542200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:21542000-21542200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:21542000-21542200	Enhancers	Fetal Intestine Large	intestine
24	chr9:21542000-21542200	Enhancers	Fetal Intestine Small	intestine
25	chr9:21542000-21542200	ZNF genes & repeats	A549	lung
26	chr9:21542000-21542200	ZNF genes & repeats	HUVEC	blood vessel
27	chr9:21542000-21542800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:21542000-21543400	Genic enhancers	NHEK	skin
29	chr9:21542000-21543600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr9:21542000-21543600	Genic enhancers	Osteobl	bone
31	chr9:21542000-21544200	Genic enhancers	HMEC	breast
32	chr9:21542000-21545400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links