Variant report

Variant	rs2553440
Chromosome Location	chr4:106792380-106792381
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106791438..106793110-chr4:106795222..106798127,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10020333	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10516523	1.00[JPT][hapmap]
rs11722731	1.00[JPT][hapmap]
rs11933386	0.86[ASN][1000 genomes]
rs11933393	0.86[ASN][1000 genomes]
rs11933466	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs11934139	1.00[JPT][hapmap]
rs11941690	1.00[JPT][hapmap]
rs12639750	1.00[JPT][hapmap]
rs13120110	0.84[ASN][1000 genomes]
rs13148869	1.00[JPT][hapmap]
rs17036098	1.00[JPT][hapmap]
rs17262764	1.00[JPT][hapmap]
rs2080789	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2544395	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2544398	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs2544400	0.84[ASN][1000 genomes]
rs2544404	0.86[ASN][1000 genomes]
rs2544405	0.91[ASN][1000 genomes]
rs2544406	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs2544408	0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs2544409	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs2544410	0.84[ASN][1000 genomes]
rs2544412	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2544413	0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs2544421	0.86[ASN][1000 genomes]
rs2544423	0.84[ASN][1000 genomes]
rs2544425	0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs2553432	0.84[ASN][1000 genomes]
rs2553434	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs2553438	0.83[ASN][1000 genomes]
rs2553441	0.93[ASN][1000 genomes]
rs2553449	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[ASN][1000 genomes]
rs2553453	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs2553454	0.83[ASN][1000 genomes]
rs2553458	1.00[JPT][hapmap]
rs2553468	1.00[JPT][hapmap]
rs2553472	0.86[ASN][1000 genomes]
rs4699196	1.00[JPT][hapmap]
rs6533218	1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs6820200	1.00[JPT][hapmap]
rs7684839	1.00[JPT][hapmap]
rs7685231	1.00[JPT][hapmap]
rs7690167	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	nsv830028	chr4:106769299-106801806	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1797065	chr4:106769322-106799532	Enhancers Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2553440	CXXC4	cis	cerebellum	SCAN
rs2553440	GAR1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106788600-106792800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:106792200-106793800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:106792200-106815800	Weak transcription	Aorta	Aorta

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