Variant report

Variant	rs41789
Chromosome Location	chr7:116491991-116491992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:116489692..116492120-chr7:116494746..116498644,3	K562	blood:
2	7:115847372-115857098..7:116489442-116492712	H1-hESC	embryonic stem cell:	embryo
3	7:115890993-115892266..7:116489442-116492712	H1-hESC	embryonic stem cell:	embryo
4	chr7:116490898..116492806-chr7:116495021..116497096,2	K562	blood:

Variant related genes	Relation type
ENSG00000135269	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11770163	0.81[JPT][hapmap]
rs12665999	0.85[YRI][hapmap]
rs12666016	0.86[YRI][hapmap]
rs1356	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1621	0.81[JPT][hapmap]
rs28167	0.87[ASN][1000 genomes]
rs28896	0.87[ASN][1000 genomes]
rs41741	0.81[JPT][hapmap]
rs41750	0.88[CHB][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.82[ASN][1000 genomes]
rs41773	0.87[ASN][1000 genomes]
rs41776	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41778	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41779	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41781	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41783	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41784	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41786	0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41791	0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41792	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41793	0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs42230	0.83[EUR][1000 genomes]
rs42338	0.82[EUR][1000 genomes]
rs42375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv831107	chr7:116414734-116649466	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41789	CASP4	trans	parietal	SCAN
rs41789	KCND2	cis	parietal	SCAN
rs41789	MET	cis	Artery Aorta	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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