Variant report

Variant	rs343699
Chromosome Location	chr6:80621654-80621655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1007416	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs13191201	0.99[ASN][1000 genomes]
rs13199685	0.95[ASN][1000 genomes]
rs13201038	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13207287	0.97[ASN][1000 genomes]
rs13216035	0.99[ASN][1000 genomes]
rs1398161	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1398162	0.98[ASN][1000 genomes]
rs1398163	0.97[ASN][1000 genomes]
rs1398164	0.97[ASN][1000 genomes]
rs1512118	0.97[ASN][1000 genomes]
rs151666	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs151667	0.96[ASN][1000 genomes]
rs151669	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151671	0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs16891260	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs1742475	0.96[ASN][1000 genomes]
rs2322554	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs239517	0.95[ASN][1000 genomes]
rs239520	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs239521	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs239523	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs239524	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs239526	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs239527	0.96[ASN][1000 genomes]
rs239528	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs239529	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs239532	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2991	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs343618	0.96[ASN][1000 genomes]
rs343620	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs343623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs343627	0.96[ASN][1000 genomes]
rs343628	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs343629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343632	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343693	1.00[ASN][1000 genomes]
rs343694	1.00[ASN][1000 genomes]
rs343696	1.00[ASN][1000 genomes]
rs343697	1.00[ASN][1000 genomes]
rs343698	1.00[ASN][1000 genomes]
rs343705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35163932	0.96[ASN][1000 genomes]
rs36067513	0.97[ASN][1000 genomes]
rs3812153	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs4706819	0.97[ASN][1000 genomes]
rs6454139	0.97[ASN][1000 genomes]
rs6915142	0.89[CHB][hapmap]
rs6928446	0.97[ASN][1000 genomes]
rs71565059	0.97[ASN][1000 genomes]
rs7743696	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs7754628	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs7754984	0.95[ASN][1000 genomes]
rs7770586	0.96[ASN][1000 genomes]
rs865264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9443725	0.99[ASN][1000 genomes]
rs9443726	0.97[ASN][1000 genomes]
rs9448853	0.99[ASN][1000 genomes]
rs9448857	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9448858	0.97[ASN][1000 genomes]
rs9448861	0.97[ASN][1000 genomes]
rs9448862	0.97[ASN][1000 genomes]
rs9448863	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv3475140	chr6:80592690-80679283	Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3475142	chr6:80592789-80679132	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs343699	LCA5	cis	cerebellum	SCAN
rs343699	ELOVL4	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80617600-80625600	Weak transcription	Fetal Thymus	thymus
2	chr6:80618400-80622600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:80618400-80656000	Weak transcription	Aorta	Aorta
4	chr6:80618600-80626200	Weak transcription	Thymus	Thymus
5	chr6:80619200-80631800	Weak transcription	Esophagus	oesophagus
6	chr6:80620200-80622600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr6:80620600-80621800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:80620600-80628400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:80620800-80621800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:80620800-80621800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:80620800-80622000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:80620800-80623000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:80620800-80628400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:80620800-80628600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:80621000-80622600	Weak transcription	Dnd41	blood
16	chr6:80621000-80630000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:80621200-80630400	Weak transcription	Ovary	ovary
18	chr6:80621400-80621800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:80621600-80622400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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