Variant report

Variant	rs3000144
Chromosome Location	chr1:79958872-79958873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10874038	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11811462	0.83[ASN][1000 genomes]
rs12021904	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023367	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12027718	0.83[ASN][1000 genomes]
rs12027888	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12027892	0.91[ASN][1000 genomes]
rs12029642	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12030013	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12034665	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036690	0.83[EUR][1000 genomes]
rs12036905	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039488	0.91[ASN][1000 genomes]
rs12039867	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039923	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040033	0.83[ASN][1000 genomes]
rs12040121	0.91[ASN][1000 genomes]
rs12040237	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040880	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041108	0.95[EUR][1000 genomes]
rs12041180	1.00[ASN][1000 genomes]
rs12041732	0.95[EUR][1000 genomes]
rs12042159	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043955	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044515	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044896	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044901	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045663	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045991	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046726	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047490	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12047951	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048746	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12049068	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389945	0.85[AFR][1000 genomes]
rs1603126	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17103209	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103224	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103273	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103305	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17103314	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2088103	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132054	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000134	0.83[ASN][1000 genomes]
rs3000143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000145	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000146	1.00[ASN][1000 genomes]
rs3000157	0.83[ASN][1000 genomes]
rs3015018	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015069	0.83[ASN][1000 genomes]
rs9425165	0.89[EUR][1000 genomes];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	nsv1004014	chr1:79811049-80042309	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1012004	chr1:79945395-80096748	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv535017	chr1:79945395-80096748	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1012296	chr1:79945395-80300216	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1005022	chr1:79950774-80106902	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79951600-79960400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:79956200-79960000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:79956200-79960000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:79956400-79959800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:79958200-79960000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:79958600-79959600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:79958800-79959200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:79958800-79960200	Active TSS	HUES48 Cell Line	embryonic stem cell

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