Variant report

Variant	rs62469223
Chromosome Location	chr7:107990269-107990270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:107988114..107994277-chr7:108093987..108097676,13	MCF-7	breast:
2	chr7:107855172..107857535-chr7:107989260..107991457,2	MCF-7	breast:
3	chr7:107988643..107991410-chr7:108016162..108018347,3	MCF-7	breast:
4	chr7:107978588..107983755-chr7:107986747..107990779,6	MCF-7	breast:
5	chr7:107840521..107844716-chr7:107989632..107993969,4	MCF-7	breast:
6	chr7:107987885..107990845-chr7:108010593..108012705,3	MCF-7	breast:
7	chr7:107984388..107993798-chr7:108093279..108099270,17	MCF-7	breast:
8	chr7:107979669..107981682-chr7:107989556..107992605,3	MCF-7	breast:
9	chr7:107976217..107977976-chr7:107988714..107990446,2	MCF-7	breast:
10	chr7:107843916..107845660-chr7:107990160..107992997,2	MCF-7	breast:
11	chr7:107988750..107990727-chr7:108091201..108092929,2	MCF-7	breast:
12	chr7:107936793..107941797-chr7:107984945..107993863,13	MCF-7	breast:
13	chr7:107965337..107967353-chr7:107989055..107990953,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10487846	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10487849	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10487851	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10953562	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953564	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12056165	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12154914	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12669401	0.90[EUR][1000 genomes]
rs12669405	0.91[EUR][1000 genomes]
rs17418660	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17419000	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17419221	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17419906	0.84[EUR][1000 genomes]
rs2267882	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2267886	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284285	0.91[EUR][1000 genomes]
rs2300015	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2300016	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2300017	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2300028	0.91[EUR][1000 genomes]
rs2300032	0.91[EUR][1000 genomes]
rs2300033	0.84[EUR][1000 genomes]
rs4727709	0.91[EUR][1000 genomes]
rs56056000	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60830378	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62469224	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62469225	0.90[EUR][1000 genomes]
rs66526866	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67033131	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67101551	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67652370	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68029971	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6942944	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6967405	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7784390	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7789982	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1019059	chr7:107935905-107995523	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1021783	chr7:107935905-107998281	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv2761354	chr7:107935905-107998293	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv1031824	chr7:107935905-108006038	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1017288	chr7:107939739-108000837	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62469223	NRCAM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107986600-107998200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:107988000-108001000	Weak transcription	HSMMtube	muscle
3	chr7:107988200-107991600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr7:107988200-107992600	Enhancers	A549	lung
5	chr7:107988400-107990400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:107988800-107994200	Weak transcription	Pancreas	Pancrea
7	chr7:107989200-107997800	Weak transcription	Placenta	Placenta
8	chr7:107989600-107991800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:107989800-107991800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr7:107989800-107992400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:107989800-107999000	Weak transcription	HMEC	breast

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