Variant report

Variant	rs16865298
Chromosome Location	chr1:175013165-175013166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10489333	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs10912849	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs10912850	0.89[CHB][hapmap]
rs10912870	0.89[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12065854	0.89[CHB][hapmap]
rs12088588	0.86[ASN][1000 genomes]
rs12562194	0.81[ASN][1000 genomes]
rs12565944	0.80[ASN][1000 genomes]
rs16847633	0.84[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap]
rs16847706	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs16847812	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs61828156	0.80[ASN][1000 genomes]
rs6662806	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6667611	0.83[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap]
rs6676700	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011472	chr1:175013165-175042885	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs16865298	KLHL20	cis	parietal	SCAN
rs16865298	RABGAP1L	cis	parietal	SCAN
rs16865298	DNM3	cis	parietal	SCAN
rs16865298	ANKRD45	cis	parietal	SCAN
rs16865298	LOC646870	cis	parietal	SCAN
rs16865298	PRDX6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174993200-175013800	Weak transcription	Spleen	Spleen
2	chr1:175012000-175014200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:175012600-175013400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
4	chr1:175013000-175013400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:175013000-175013400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:175013000-175013400	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr1:175013000-175013400	Enhancers	Fetal Stomach	stomach
8	chr1:175013000-175013600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:175013000-175013600	Enhancers	Fetal Muscle Trunk	muscle
10	chr1:175013000-175013800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:175013000-175013800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:175013000-175013800	Enhancers	Fetal Lung	lung
13	chr1:175013000-175014000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:175013000-175014000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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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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