Variant report

Variant	rs3128364
Chromosome Location	chr1:112840578-112840579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10857952	0.87[ASN][1000 genomes]
rs12127798	0.88[ASN][1000 genomes]
rs2998335	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3005799	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3121989	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3124030	0.81[ASN][1000 genomes]
rs3128365	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3128366	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3128367	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3128371	0.86[ASN][1000 genomes]
rs3128373	0.81[ASN][1000 genomes]
rs4294408	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4433390	0.88[ASN][1000 genomes]
rs5021965	0.87[ASN][1000 genomes]
rs6676747	0.91[ASN][1000 genomes]
rs9429470	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv2454	chr1:112813849-112858259	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv508526	chr1:112839396-112915215	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3128364	AHCYL1	cis	cerebellum	SCAN
rs3128364	CSDE1	cis	cerebellum	SCAN
rs3128364	SLC6A17	cis	cerebellum	SCAN
rs3128364	CEPT1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112839600-112840600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr1:112839600-112840800	Enhancers	HSMM	muscle
3	chr1:112840200-112840800	Enhancers	NHEK	skin
4	chr1:112840200-112841000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:112840200-112841000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:112840400-112841200	Enhancers	Brain Germinal Matrix	brain
7	chr1:112840400-112841200	Enhancers	HMEC	breast
8	chr1:112840400-112841400	Weak transcription	HSMMtube	muscle

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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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