Variant report

Variant	rs1157178
Chromosome Location	chr5:119884992-119884993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10045601	0.93[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs1037572	0.87[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs1039546	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs10519637	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11241548	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs11241549	0.93[CEU][hapmap];0.83[CHD][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs1157177	1.00[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13165484	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13170550	0.87[EUR][1000 genomes]
rs1454981	0.93[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs1524576	0.93[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2124162	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2168215	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs300966	0.87[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4895262	1.00[CEU][hapmap];0.80[CHB][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6862351	0.86[EUR][1000 genomes]
rs7706727	0.93[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs874946	0.86[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830463	chr5:119806643-119968825	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv462427	chr5:119838923-119928674	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599601	chr5:119838923-119928674	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1031453	chr5:119843593-120393038	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv948613	chr5:119861955-119999008	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv599602	chr5:119866504-120023393	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv949499	chr5:119869763-119999008	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv882787	chr5:119874306-119925692	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1157178	SNX2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119874800-119886000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:119880000-119885200	Weak transcription	NH-A	brain
3	chr5:119880000-119903000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:119880600-119886000	Weak transcription	Left Ventricle	heart
5	chr5:119881200-119885400	Weak transcription	HSMM	muscle
6	chr5:119881200-119885600	Weak transcription	NHLF	lung
7	chr5:119882000-119891000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:119882200-119903800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:119883800-119890600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:119884200-119885200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:119884400-119885000	Enhancers	Psoas Muscle	Psoas
12	chr5:119884400-119886400	Enhancers	NHDF-Ad	bronchial
13	chr5:119884400-119890600	Enhancers	Osteobl	bone
14	chr5:119884600-119886000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:119884600-119886200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:119884800-119888000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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