Variant report

Variant	rs1842394
Chromosome Location	chr3:51356217-51356218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10510757	0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs10510758	0.86[ASN][1000 genomes]
rs12485610	0.81[ASN][1000 genomes]
rs12487426	0.81[ASN][1000 genomes]
rs12487468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12489219	0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12489414	0.85[ASN][1000 genomes]
rs12490471	0.81[ASN][1000 genomes]
rs12490889	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12491048	0.88[ASN][1000 genomes]
rs12492615	0.94[CHB][hapmap]
rs12492624	0.81[ASN][1000 genomes]
rs12493034	0.88[AMR][1000 genomes]
rs12493323	0.87[CHB][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12493618	0.85[ASN][1000 genomes]
rs12493857	0.81[ASN][1000 genomes]
rs12493978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12494462	0.81[ASN][1000 genomes]
rs12494979	0.86[ASN][1000 genomes]
rs12495561	0.89[CHB][hapmap];0.88[AMR][1000 genomes]
rs13090348	0.85[ASN][1000 genomes]
rs1370124	0.87[ASN][1000 genomes]
rs17051783	0.86[ASN][1000 genomes]
rs17051799	0.82[YRI][hapmap]
rs17661242	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17712228	0.85[ASN][1000 genomes]
rs1809388	0.88[AMR][1000 genomes]
rs2033703	0.84[ASN][1000 genomes]
rs2086395	0.88[AMR][1000 genomes]
rs2101056	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs2127654	0.83[AMR][1000 genomes]
rs2170177	0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2217938	0.86[ASN][1000 genomes]
rs2241785	0.88[ASN][1000 genomes]
rs2304512	0.86[ASN][1000 genomes]
rs2306430	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2306431	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2355946	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2356261	0.86[ASN][1000 genomes]
rs2356298	0.81[ASN][1000 genomes]
rs3749317	0.86[ASN][1000 genomes]
rs3762711	0.88[AMR][1000 genomes]
rs3792408	0.86[ASN][1000 genomes]
rs3804766	0.86[ASN][1000 genomes]
rs3828395	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4130473	0.95[CHB][hapmap]
rs4346580	0.88[CHB][hapmap]
rs4468966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4687601	0.86[ASN][1000 genomes]
rs4687605	0.81[ASN][1000 genomes]
rs4687610	0.85[ASN][1000 genomes]
rs4687731	0.86[ASN][1000 genomes]
rs4687777	0.86[ASN][1000 genomes]
rs4687811	0.85[ASN][1000 genomes]
rs4687812	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4687813	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4974096	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4974112	0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56052360	0.88[AMR][1000 genomes]
rs56239081	0.81[ASN][1000 genomes]
rs56729479	0.81[ASN][1000 genomes]
rs57027950	0.85[ASN][1000 genomes]
rs57047724	0.89[ASN][1000 genomes]
rs57603251	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs57831708	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58059174	0.81[ASN][1000 genomes]
rs58201844	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58568178	0.83[ASN][1000 genomes]
rs58836277	0.86[ASN][1000 genomes]
rs58911602	0.88[AMR][1000 genomes]
rs59129045	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59563413	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59953568	0.91[ASN][1000 genomes]
rs60128296	0.83[AMR][1000 genomes]
rs60567238	0.88[AMR][1000 genomes]
rs60606339	0.81[ASN][1000 genomes]
rs60740654	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61419317	0.86[ASN][1000 genomes]
rs61660900	0.88[AMR][1000 genomes]
rs72936442	0.86[AMR][1000 genomes]
rs72936462	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72945708	0.84[ASN][1000 genomes]
rs72945713	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72953175	0.88[AMR][1000 genomes]
rs73834252	0.86[ASN][1000 genomes]
rs73834253	0.82[ASN][1000 genomes]
rs73834254	0.82[ASN][1000 genomes]
rs73834258	0.81[ASN][1000 genomes]
rs73837439	0.91[ASN][1000 genomes]
rs73837442	0.86[ASN][1000 genomes]
rs73837443	0.86[ASN][1000 genomes]
rs751076	0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs880478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9817077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9817872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9820140	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9829057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9856134	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9878592	0.88[CHB][hapmap];0.88[AMR][1000 genomes]
rs9880909	0.87[YRI][hapmap]

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:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51340000-51370800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:51341600-51372000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:51344200-51371800	Weak transcription	Brain Substantia Nigra	brain
4	chr3:51345000-51356400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:51345600-51358000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:51348000-51356400	Weak transcription	HSMMtube	muscle
7	chr3:51349400-51358600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:51351800-51367600	Weak transcription	Brain Anterior Caudate	brain
9	chr3:51351800-51369200	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:51352800-51369800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:51353000-51357400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:51353000-51370000	Weak transcription	Brain Germinal Matrix	brain
13	chr3:51353000-51370200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:51353200-51367600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:51353200-51370200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:51353400-51369400	Weak transcription	Fetal Brain Female	brain
17	chr3:51353400-51375800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:51353400-51377600	Weak transcription	Left Ventricle	heart
19	chr3:51353800-51367600	Weak transcription	Brain Cingulate Gyrus	brain

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