Variant report

Variant	rs2972934
Chromosome Location	chr5:37788861-37788862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1862574	0.85[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2910702	0.85[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2910709	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2910712	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2910800	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2973038	0.82[ASN][1000 genomes]
rs2973043	0.80[CHB][hapmap]
rs2973059	0.86[ASN][1000 genomes]
rs2973060	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3096140	0.80[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs3749692	0.87[CHD][hapmap];0.81[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	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2972934	NIPBL	cis	cerebellum	SCAN
rs2972934	C9	cis	parietal	SCAN
rs2972934	UGT3A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37786000-37790600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:37787200-37793000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:37787600-37789400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:37787600-37790600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:37787600-37791800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:37787600-37792800	Weak transcription	NHLF	lung
7	chr5:37787800-37793000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:37788000-37790000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:37788000-37790200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:37788000-37792800	Weak transcription	NH-A	brain
11	chr5:37788000-37793000	Weak transcription	HSMMtube	muscle
12	chr5:37788200-37792600	Weak transcription	NHDF-Ad	bronchial
13	chr5:37788200-37792800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:37788200-37793000	Weak transcription	HMEC	breast
15	chr5:37788400-37792800	Weak transcription	HSMM	muscle
16	chr5:37788800-37792600	Weak transcription	Osteobl	bone

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Input of quick search could be:

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

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