Variant report

Variant	rs2239956
Chromosome Location	chr7:116949286-116949287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10953841	0.82[CHB][hapmap]
rs17347210	0.82[YRI][hapmap]
rs2285543	0.93[ASN][1000 genomes]
rs2285544	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2285545	0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs254536	0.82[CHB][hapmap]
rs39312	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs39315	0.82[CHB][hapmap]
rs39317	0.82[CHB][hapmap]
rs39324	0.82[CHB][hapmap]
rs4727848	0.94[ASN][1000 genomes]
rs6946481	0.96[ASN][1000 genomes]
rs6947329	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs739517	0.82[CHB][hapmap]

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	nsv831108	chr7:116749534-116952011	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv608256	chr7:116928371-117040117	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2239956	PXN	trans	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116931800-116961600	Weak transcription	Placenta	Placenta
2	chr7:116936400-116952200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:116937000-116954800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr7:116945200-116954400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:116946800-116951000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:116946800-116951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:116946800-116951800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:116946800-116951800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:116947000-116951200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:116947600-116951600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:116948800-116950200	Strong transcription	Fetal Lung	lung

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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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