Variant report

Variant	rs3823990
Chromosome Location	chr7:103133201-103133202
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:103114323..103116604-chr7:103131705..103134120,2	K562	blood:
2	chr7:103131065..103134051-chr7:103136499..103139382,2	K562	blood:
3	chr7:103133035..103134783-chr7:103139983..103142460,3	K562	blood:
4	chr7:103133039..103134783-chr7:103140614..103142460,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10085736	0.81[CEU][hapmap];0.94[CHB][hapmap];0.80[EUR][1000 genomes]
rs1024559	0.94[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10262559	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10282605	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs11971743	0.81[ASN][1000 genomes]
rs11979750	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11979752	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11983689	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12705123	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13229533	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13232021	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13235135	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13239318	0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17150781	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17152161	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2079469	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2237622	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2528873	0.83[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2528875	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2711865	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs2711882	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2711883	0.88[CHB][hapmap];0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs2711887	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34079239	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34953117	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35246772	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35603368	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56345626	0.83[ASN][1000 genomes]
rs62480384	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7804453	0.93[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7808106	0.83[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][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	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3823990	CUX1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103118400-103138000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:103122800-103141000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:103129000-103134800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:103129800-103133400	Weak transcription	Stomach Mucosa	stomach
5	chr7:103130800-103135800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:103130800-103155000	Weak transcription	Brain Substantia Nigra	brain
7	chr7:103130800-103163600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:103131200-103136200	Weak transcription	HepG2	liver
9	chr7:103131200-103137000	Weak transcription	Brain Anterior Caudate	brain
10	chr7:103131200-103145000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:103131400-103138000	Weak transcription	K562	blood

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