Variant report

Variant	rs62276884
Chromosome Location	chr3:98696107-98696108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr3:98696034-98697098	SK-N-SH	brain:	n/a	n/a
2	EP300	chr3:98696092-98697028	SK-N-SH	brain:	n/a	chr3:98696636-98696645 chr3:98696637-98696646 chr3:98696403-98696417
3	SP1	chr3:98696091-98697005	HCT-116	colon:	n/a	chr3:98696599-98696608
4	JUND	chr3:98696003-98697007	HCT-116	colon:	n/a	chr3:98696637-98696646 chr3:98696635-98696647 chr3:98696635-98696646 chr3:98696636-98696646 chr3:98696637-98696645 chr3:98696633-98696644 chr3:98696638-98696645
5	FOSL1	chr3:98696039-98697250	HCT-116	colon:	n/a	chr3:98697196-98697208 chr3:98696637-98696646 chr3:98696635-98696647 chr3:98696636-98696646 chr3:98696637-98696645 chr3:98696633-98696644 chr3:98696638-98696645
6	BCL3	chr3:98696078-98697480	A549	lung:	n/a	chr3:98696636-98696645 chr3:98696637-98696646
7	EP300	chr3:98696085-98697051	SK-N-SH	brain:	n/a	chr3:98696636-98696645 chr3:98696637-98696646 chr3:98696403-98696417
8	EP300	chr3:98696076-98697519	A549	lung:	n/a	chr3:98697459-98697469 chr3:98697256-98697270 chr3:98697299-98697307 chr3:98696636-98696645 chr3:98696637-98696646 chr3:98696403-98696417
9	GATA3	chr3:98696060-98697575	A549	lung:	n/a	n/a
10	FOXM1	chr3:98696064-98697105	ECC-1	luminal epithelium:	n/a	n/a
11	SIX5	chr3:98696053-98696907	A549	lung:	n/a	n/a
12	SP1	chr3:98696040-98697362	HCT-116	colon:	n/a	chr3:98696599-98696608
13	CEBPB	chr3:98696094-98696855	HCT-116	colon:	n/a	chr3:98696405-98696418
14	NFIC	chr3:98696103-98697040	SK-N-SH	brain:	n/a	n/a
15	FOXM1	chr3:98696104-98697013	ECC-1	luminal epithelium:	n/a	n/a
16	CEBPB	chr3:98696057-98697101	HCT-116	colon:	n/a	chr3:98696405-98696418

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98695632..98696208-chr9:117342465..117342965,2	HCT-116	colon:

Variant related genes	Relation type
LINC00973	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10433438	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10511169	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10511171	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935518	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935542	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935564	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935610	0.84[AMR][1000 genomes]
rs11708475	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716000	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11716007	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716281	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716579	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11719660	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914591	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918243	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11918944	1.00[ASN][1000 genomes]
rs11920205	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920327	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11922078	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923486	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923805	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928233	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069458	1.00[ASN][1000 genomes]
rs1471588	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16840260	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17212369	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17213336	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278047	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17278278	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17852693	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1827158	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55650073	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55662129	0.91[ASN][1000 genomes]
rs55730510	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55764252	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55988144	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56290036	0.91[ASN][1000 genomes]
rs56322058	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276861	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276862	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276864	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276869	1.00[ASN][1000 genomes]
rs62276879	0.94[ASN][1000 genomes]
rs62276883	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276885	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276888	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276909	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276944	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440253	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66517942	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805605	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73138027	0.91[ASN][1000 genomes]
rs73138030	0.91[ASN][1000 genomes]
rs73138048	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73138053	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73138055	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73138058	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73138063	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73138082	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73140009	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73140027	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73140032	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7432439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614892	0.91[ASN][1000 genomes]
rs7629550	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7638009	1.00[ASN][1000 genomes]
rs7642785	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs982291	1.00[ASN][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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98691000-98696200	Weak transcription	Hela-S3	cervix
2	chr3:98691400-98696400	Weak transcription	HSMM	muscle
3	chr3:98691600-98696400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:98691800-98696400	Weak transcription	NHLF	lung
5	chr3:98692000-98696200	Weak transcription	NHEK	skin
6	chr3:98692000-98696400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:98692000-98699600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:98693600-98696400	Weak transcription	NHDF-Ad	bronchial
9	chr3:98693600-98697400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:98695000-98696400	Enhancers	A549	lung
11	chr3:98695000-98696400	Enhancers	HUVEC	blood vessel
12	chr3:98695000-98697800	Enhancers	HMEC	breast
13	chr3:98695200-98696400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:98695200-98696400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:98695400-98698800	Enhancers	Osteobl	bone
16	chr3:98695600-98696400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:98695600-98696600	Weak transcription	NH-A	brain
18	chr3:98695600-98696800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:98695800-98696200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:98696000-98696400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:98696000-98696400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:98696000-98696600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:98696000-98697200	Enhancers	HSMMtube	muscle
24	chr3:98696000-98699600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links