Variant report

Variant	rs2378331
Chromosome Location	chr1:220078828-220078829
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10863510	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863511	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1694592	0.94[CEU][hapmap];0.91[JPT][hapmap]
rs1694594	0.94[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs1694595	0.93[CEU][hapmap];0.81[JPT][hapmap]
rs1776029	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1776030	0.84[ASN][1000 genomes]
rs1776043	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1776046	0.94[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap]
rs1776050	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2275706	0.81[JPT][hapmap]
rs2275707	0.94[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs6541114	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6541115	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663638	0.82[EUR][1000 genomes]
rs6663745	0.82[EUR][1000 genomes]
rs947517	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006393	chr1:219925261-220126458	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1067840	chr1:219990803-220091941	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2378331	GPATCH2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220077000-220080400	Weak transcription	HepG2	liver
2	chr1:220077400-220080600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:220077400-220086800	Weak transcription	Fetal Intestine Large	intestine
4	chr1:220077400-220088400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:220077400-220088600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:220078200-220079000	Enhancers	K562	blood

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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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