Variant report

Variant	rs837400
Chromosome Location	chr1:47265776-47265777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10890422	0.81[CHB][hapmap];0.84[CHD][hapmap];0.85[TSI][hapmap]
rs1097608	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2297812	0.81[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs4646485	0.81[CHB][hapmap];0.84[CHD][hapmap];0.80[TSI][hapmap]
rs632233	0.88[YRI][hapmap]
rs837399	0.84[ASN][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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1011086	chr1:47259078-47305191	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv870792	chr1:47259138-47272185	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv870538	chr1:47259138-47309265	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1010063	chr1:47264205-47285118	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs837400	GPBP1L1	cis	cerebellum	SCAN
rs837400	SLC6A9	cis	parietal	SCAN
rs837400	HECTD3	cis	cerebellum	SCAN
rs837400	CCNYL1	trans	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47264400-47265800	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr1:47264600-47269200	Active TSS	Left Ventricle	heart
3	chr1:47264800-47265800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
4	chr1:47264800-47266800	Active TSS	Esophagus	oesophagus
5	chr1:47265200-47265800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:47265200-47267200	Active TSS	Lung	lung
7	chr1:47265200-47267400	Weak transcription	Stomach Mucosa	stomach
8	chr1:47265400-47268600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:47265400-47271400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:47265600-47265800	Active TSS	Right Atrium	heart
11	chr1:47265600-47266400	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:47265600-47268800	Active TSS	Psoas Muscle	Psoas
13	chr1:47265600-47271800	Weak transcription	Spleen	Spleen
14	chr1:47265600-47279200	Weak transcription	Gastric	stomach

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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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