Variant report

Variant	rs2437879
Chromosome Location	chr6:81235716-81235717
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1436867	0.82[EUR][1000 genomes]
rs1436868	0.88[EUR][1000 genomes]
rs1698337	0.82[EUR][1000 genomes]
rs1816564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865917	0.82[EUR][1000 genomes]
rs2164606	0.82[EUR][1000 genomes]
rs2164607	0.82[EUR][1000 genomes]
rs2164608	0.82[EUR][1000 genomes]
rs2917605	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917606	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917607	0.82[EUR][1000 genomes]
rs2917608	0.82[EUR][1000 genomes]
rs3011299	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3011300	0.82[EUR][1000 genomes]
rs3011301	0.86[EUR][1000 genomes]
rs3011302	0.88[EUR][1000 genomes]
rs3011304	0.82[EUR][1000 genomes]
rs484560	0.82[EUR][1000 genomes]
rs486271	0.82[EUR][1000 genomes]
rs487328	0.82[EUR][1000 genomes]
rs506825	0.82[EUR][1000 genomes]
rs508759	0.82[EUR][1000 genomes]
rs512946	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520099	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520139	0.82[EUR][1000 genomes]
rs522183	0.82[EUR][1000 genomes]
rs526071	0.89[CEU][hapmap]
rs528886	0.82[EUR][1000 genomes]
rs529744	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532709	0.82[EUR][1000 genomes]
rs535350	0.82[EUR][1000 genomes]
rs540896	0.81[EUR][1000 genomes]
rs553433	0.82[EUR][1000 genomes]
rs558478	0.89[CEU][hapmap]
rs559034	0.81[EUR][1000 genomes]
rs560068	0.82[EUR][1000 genomes]
rs560909	0.82[EUR][1000 genomes]
rs564757	0.82[EUR][1000 genomes]
rs567324	0.89[CEU][hapmap]
rs568155	0.82[EUR][1000 genomes]
rs572007	0.82[EUR][1000 genomes]
rs577129	0.82[EUR][1000 genomes]
rs577892	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs580525	0.82[EUR][1000 genomes]
rs584904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.93[LWK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs593167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594567	0.82[EUR][1000 genomes]
rs595791	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596723	0.89[CEU][hapmap]
rs597937	0.82[EUR][1000 genomes]
rs597950	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs610292	0.82[EUR][1000 genomes]
rs615815	0.82[EUR][1000 genomes]
rs622089	0.82[EUR][1000 genomes]
rs622117	0.82[EUR][1000 genomes]
rs622849	0.82[EUR][1000 genomes]
rs623286	0.82[EUR][1000 genomes]
rs623367	0.82[EUR][1000 genomes]
rs624645	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs625136	0.82[EUR][1000 genomes]
rs630687	0.82[EUR][1000 genomes]
rs631481	0.82[EUR][1000 genomes]
rs632397	0.82[EUR][1000 genomes]
rs645216	0.82[EUR][1000 genomes]
rs654625	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs654955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655350	0.82[EUR][1000 genomes]
rs656381	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs661076	0.82[EUR][1000 genomes]
rs661119	0.82[EUR][1000 genomes]
rs66969849	0.82[EUR][1000 genomes]
rs67220910	0.82[EUR][1000 genomes]
rs674031	0.82[EUR][1000 genomes]
rs675769	0.82[EUR][1000 genomes]
rs681085	0.83[ASN][1000 genomes]
rs687203	0.82[EUR][1000 genomes]
rs694288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694756	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73473458	0.82[EUR][1000 genomes]
rs9352838	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs9443781	0.82[EUR][1000 genomes]
rs9449007	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531333	chr6:81042427-81836484	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1019670	chr6:81086504-81569984	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv915714	chr6:81134888-81366749	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv886311	chr6:81166178-81239971	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv886312	chr6:81166178-81309481	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv886313	chr6:81177227-81239971	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv463908	chr6:81232993-81287675	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv604054	chr6:81232993-81287675	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2437879	LCA5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:81230400-81237800	Weak transcription	Pancreas	Pancrea
2	chr6:81232400-81235800	Enhancers	Fetal Brain Male	brain
3	chr6:81232800-81237000	Weak transcription	Fetal Lung	lung
4	chr6:81233400-81237400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:81233600-81249600	Weak transcription	HSMM	muscle
6	chr6:81233800-81237800	Weak transcription	NHDF-Ad	bronchial
7	chr6:81234000-81237000	Weak transcription	Hela-S3	cervix
8	chr6:81234000-81237400	Weak transcription	Fetal Heart	heart
9	chr6:81234000-81237600	Weak transcription	Small Intestine	intestine
10	chr6:81234000-81238000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:81234200-81236400	Weak transcription	HepG2	liver
12	chr6:81234200-81237200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:81234200-81237600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:81234200-81237800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:81234200-81239200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:81234200-81245000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:81234200-81245200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:81234200-81249600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:81235600-81236400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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