Variant report

Variant	rs7642077
Chromosome Location	chr3:51382601-51382602
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]
rs17051747	0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051755	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55640023	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55699461	1.00[EUR][1000 genomes]
rs55708856	1.00[EUR][1000 genomes]
rs56037427	1.00[EUR][1000 genomes]
rs56254449	1.00[EUR][1000 genomes]
rs56361536	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56870664	1.00[EUR][1000 genomes]
rs56940802	1.00[EUR][1000 genomes]
rs57569631	0.93[AFR][1000 genomes]
rs57742040	1.00[EUR][1000 genomes]
rs58236908	1.00[EUR][1000 genomes]
rs58548979	1.00[EUR][1000 genomes]
rs59019902	1.00[EUR][1000 genomes]
rs59557845	1.00[EUR][1000 genomes]
rs59599274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59652730	1.00[EUR][1000 genomes]
rs59794491	1.00[EUR][1000 genomes]
rs60166061	1.00[EUR][1000 genomes]
rs60862896	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60973580	1.00[EUR][1000 genomes]
rs61337570	1.00[EUR][1000 genomes]
rs61526358	1.00[EUR][1000 genomes]
rs61570923	1.00[EUR][1000 genomes]
rs6781959	1.00[EUR][1000 genomes]
rs6799213	1.00[EUR][1000 genomes]
rs6804101	1.00[EUR][1000 genomes]
rs73833980	1.00[EUR][1000 genomes]
rs73833981	1.00[EUR][1000 genomes]
rs73833982	1.00[EUR][1000 genomes]
rs73833985	1.00[EUR][1000 genomes]
rs73833986	1.00[EUR][1000 genomes]
rs73833987	1.00[EUR][1000 genomes]
rs73833989	1.00[EUR][1000 genomes]
rs73833990	1.00[EUR][1000 genomes]
rs73833991	1.00[EUR][1000 genomes]
rs73833992	1.00[EUR][1000 genomes]
rs73833993	1.00[EUR][1000 genomes]
rs73833996	1.00[EUR][1000 genomes]
rs73834257	1.00[EUR][1000 genomes]
rs73837406	1.00[EUR][1000 genomes]
rs73837420	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837421	1.00[EUR][1000 genomes]
rs73837422	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837423	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837425	1.00[EUR][1000 genomes]
rs73837428	1.00[EUR][1000 genomes]
rs73837431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837432	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837433	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630259	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7635095	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9990213	0.82[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51369600-51383800	Weak transcription	Fetal Brain Male	brain
2	chr3:51376800-51391800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:51376800-51392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:51378000-51399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:51378200-51383000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:51378400-51389800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:51378600-51383000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:51378800-51383800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:51378800-51387400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:51378800-51388000	Weak transcription	Brain Angular Gyrus	brain
12	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
13	chr3:51379000-51386000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:51379000-51390200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:51379000-51393800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
17	chr3:51379200-51393600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:51379200-51393800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:51379200-51399800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:51379400-51383800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:51379400-51403400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:51380000-51398400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:51380000-51398400	Weak transcription	Aorta	Aorta
24	chr3:51380200-51383000	Enhancers	A549	lung
25	chr3:51380800-51383000	Strong transcription	Brain Hippocampus Middle	brain
26	chr3:51381000-51383000	Enhancers	NHLF	lung
27	chr3:51381200-51382800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:51381200-51382800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:51381200-51382800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:51381200-51382800	Enhancers	NHDF-Ad	bronchial
31	chr3:51381200-51383000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:51381400-51382800	Enhancers	Esophagus	oesophagus
33	chr3:51381400-51382800	Enhancers	HMEC	breast
34	chr3:51381400-51383000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:51381400-51392000	Weak transcription	Brain Anterior Caudate	brain
36	chr3:51381600-51382800	Enhancers	Stomach Mucosa	stomach
37	chr3:51381800-51387400	Weak transcription	Fetal Brain Female	brain
38	chr3:51381800-51392200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:51382000-51382800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:51382200-51382800	Enhancers	Gastric	stomach
41	chr3:51382200-51382800	Enhancers	Osteobl	bone
42	chr3:51382200-51387200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:51382400-51383200	Enhancers	Hela-S3	cervix
44	chr3:51382400-51389800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:51382600-51382800	Enhancers	Spleen	Spleen
46	chr3:51382600-51382800	Enhancers	HSMMtube	muscle
47	chr3:51382600-51386600	Weak transcription	NHEK	skin

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